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

1 files changed, 0 insertions, 142 deletions

diff --git a/web/webqtl/submitTrait/BatchSubmitPage.py b/web/webqtl/submitTrait/BatchSubmitPage.py
deleted file mode 100755
index 1c0be1ed..00000000
--- a/web/webqtl/submitTrait/BatchSubmitPage.py
+++ /dev/null
@@ -1,142 +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
-
-import glob
-from htmlgen import HTMLgen2 as HT
-import os
-
-from base.templatePage import templatePage
-from utility import webqtlUtil
-from base import webqtlConfig
-
-
-# XZ, 09/09/2008: From home, click "Batch Submission".
-# XZ, 09/09/2008: This class generate what you see		
-#########################################
-#      BatchSubmitPage
-#########################################
-
-class BatchSubmitPage(templatePage):
-
-	def __init__(self, fd):
-
-		templatePage.__init__(self, fd)
-
-		self.dict['title'] = 'Batch Submission' 
-
-		TD_LEFT = """
-		<TD vAlign=top width="40%" bgColor=#eeeeee>
-			<P class="title">Introduction</P>
-			<BLOCKQUOTE>
-				<P>The batch submission utility enables users to submit multiple
-				traits at the same time for analysis by the GeneNetwork and 
-				WebQTL. The data  will be stored on our server for no more than 
-				24 hours. None of the submitted data are stored or copied 
-				elsewhere.</P>
-				<P>The file to be uploaded should follow correct format shown 
-				in the <A Href="/sample.txt" class="normalsize" target="_blank">
-				Sample</A>, <A Href="/sample2.txt" class="normalsize" 
-				target="_blank">Sample2</A> text file.</P>
-				<P>Please follow the <A href="http://www.genenetwork.org/faq.html#Q-22" class="normalsize" target="_blank">guide</A> for naming your traits.</P>
-			</BLOCKQUOTE>
-		</TD>
-		"""
-		TD_RIGHT = HT.TD(valign="top",width="60%",bgcolor="#eeeeee")
-		main_title = HT.Paragraph("Batch Trait Submission Utility")
-		main_title.__setattr__("class","title")
-
-		#############################
-
-		title1 = HT.Paragraph("1. Choose cross or RI set:")
-		title1.__setattr__("class","subtitle")
-
-		STEP1 = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0)
-		crossMenu = HT.Select(name='RISet', onChange='xchange()')
-		allRISets = map(lambda x: x[:-5], glob.glob1(webqtlConfig.GENODIR, '*.geno'))
-		allRISets.sort()
-		allRISets.remove("BayXSha")
-		allRISets.remove("ColXBur")
-		allRISets.remove("ColXCvi")
-		specMenuSub1 = HT.Optgroup(label = 'MOUSE')
-		specMenuSub2 = HT.Optgroup(label = 'RAT')
-		for item in allRISets:
-			if item != 'HXBBXH':
-				specMenuSub1.append(tuple([item,item]))
-			else:
-				specMenuSub2.append(tuple(['HXB/BXH', 'HXBBXH']))
-		crossMenu.append(specMenuSub1)
-		crossMenu.append(specMenuSub2)
-		crossMenu.selected.append('BXD')
-		crossMenuText = HT.Paragraph('Select the cross or recombinant inbred \
-		    set from the menu below. ')
- 		infoButton = HT.Input(type="button",Class="button",value="Info",\
- 		    onClick="crossinfo2();")
-		# NL, 07/27/2010. variable 'IMGSTEP1' has been moved from templatePage.py to webqtlUtil.py;
-		TD1 = HT.TD(webqtlUtil.IMGSTEP1,width=58)
-		TD2 = HT.TD()
-		TD2.append(crossMenuText,crossMenu, infoButton)
-		STEP1.append(HT.TR(TD1,TD2),HT.TR(HT.TD(colspan=2,height=20)))
-		
-		#############################
-		title2 = HT.Paragraph("&nbsp;&nbsp;2. Enter Trait Data:")
-		title2.__setattr__("class","subtitle")
-
-		STEP2 = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0)
-		Para1 = HT.Paragraph()
-		Para1.append('You can submit traits by entering a file name here. The \
-		    file should contain a number of no more than 100 traits. The file \
-		    should follow the file format described in this ', HT.Href(url=\
-		    "/sample.txt",Class="normalsize", target="_blank", \
-		    text= 'Sample'), ' text.')
-		
-		filebox = HT.Paragraph(HT.Input(type='file', name='batchdatafile', size=20))
-
-		# NL, 07/27/2010. variable 'IMGSTEP2' has been moved from templatePage.py to webqtlUtil.py;		
-		TD1 = HT.TD(webqtlUtil.IMGSTEP2,width=58)
-		TD2 = HT.TD()
-		TD2.append(Para1,filebox)
-		STEP2.append(HT.TR(TD1,TD2),HT.TR(HT.TD(colspan=2,height=20)))
-		
-		#########################################
-		hddn = {'FormID':'batSubmitResult'}
-		
-		form = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), \
-		enctype='multipart/form-data', name='crossChoice', submit=HT.Input(type='hidden'))
-		
-		submit = HT.Input(type='button' ,name='next', value='Next',onClick=\
-		    'batchSelection(this.form);',Class="button") 			
-		reset = HT.Input(type='reset' ,name='reset' ,value='Reset',Class="button")
-		# NL, 07/27/2010. variable 'IMGNEXT' has been moved from templatePage.py to webqtlUtil.py;	
-		form.append(HT.Blockquote(title1,HT.Center(STEP1,webqtlUtil.IMGNEXT),title2,\
-		    HT.Center(STEP2,webqtlUtil.IMGNEXT)),HT.Center(HT.P(),submit,reset))
-			
-		for key in hddn.keys():
-			form.append(HT.Input(name=key, value=hddn[key], type='hidden'))
-		
-		TD_RIGHT.append(main_title,form)
-		
-		self.dict['body'] = TD_LEFT + str(TD_RIGHT)
-