Merge branch 'master' of https://github.com/zsloan/genenetwork2 into zsloan

1 files changed, 0 insertions, 222 deletions

diff --git a/wqflask/base/templatePage.py b/wqflask/base/templatePage.py
deleted file mode 100755
index a94d5153..00000000
--- a/wqflask/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'
-
-        # 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.db_conn = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, \
-                                    user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD)
-            self.cursor = self.db_conn.cursor()
-            return True
-        except Exception:
-            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 False
-
-    def updMysql(self):
-        try:
-            self.db_conn = MySQLdb.Connect(db=webqtlConfig.DB_UPDNAME,host=webqtlConfig.MYSQL_UPDSERVER, \
-                                    user=webqtlConfig.DB_UPDUSER,passwd=webqtlConfig.DB_UPDPASSWD)
-            self.cursor = self.db_conn.cursor()
-            return True
-        except Exception:
-            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 False
-
-    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