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

1 files changed, 0 insertions, 233 deletions

diff --git a/web/webqtl/submitTrait/CrossChoicePage.py b/web/webqtl/submitTrait/CrossChoicePage.py
deleted file mode 100755
index fd919e5b..00000000
--- a/web/webqtl/submitTrait/CrossChoicePage.py
+++ /dev/null
@@ -1,233 +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, 08/28/2008: From home, click "Enter Trait Data".
-# XZ, 08/28/2008: This class generate what you see	
-#########################################
-#      CrossChoicePage
-#########################################
-
-class CrossChoicePage(templatePage):
-
-	def __init__(self, fd):
-
-		templatePage.__init__(self, fd)
-
-		self.dict['title'] = 'Trait Submission'
-
-		if not self.openMysql():
-			return
-		
-		authorized = 0
-		if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['user']:
-			authorized = 1
-	
-		TD_LEFT = """
-		<TD vAlign=top width="45%" bgColor=#eeeeee>
-			<P class="title">Introduction</P>
-			<BLOCKQUOTE>
-				<P>The trait values that you enter are statistically compared 
-				with verified genotypes collected at a set of microsatellite 
-				markers in each RI set. The markers are drawn from a set of 
-				over 750, but for each set redundant markers have been removed,
-				preferentially retaining those that are most informative. </P>
-
-				<P>These error-checked RI mapping data match theoretical 
-				expectations for RI strain sets. The cumulative adjusted length
-				of the RI maps are approximately 1400 cM, a value that matches 
-				those of both MIT maps and Chromosome Committee Report maps. 
-				See our <a Href="http://www.nervenet.org/papers/BXN.html" 
-				class="normalsize"> full description</a> of the genetic data 
-				collected as part of the WebQTL project. </P>
-
-			</BLOCKQUOTE>
-			<P class="title">About Your Data</P>
-			<BLOCKQUOTE>
-				<P>You can open a separate <a Href="RIsample.html" target="_blank" 
-				class="normalsize"> window </a> giving the number of strains 
-				for each data set and sample data. </P>
-				<P>None of your submitted data is copied or stored by this 
-				system except during the actual processing of your submission. 
-				By the time the reply page displays in your browser, your 
-				submission has been cleared from this system. </P>
-			</BLOCKQUOTE>
-		</TD>
-		"""
-		TD_RIGHT = HT.TD(valign="top",width="55%",bgcolor="#eeeeee")
-		main_title = HT.Paragraph(" Trait Submission Form")
-		main_title.__setattr__("class","title")
-
-		#############################
-
-		title1 = HT.Paragraph("&nbsp;&nbsp;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()
-		if authorized:
-			self.cursor.execute("select Name from InbredSet")
-		else:
-			self.cursor.execute("select Name from InbredSet where public > %d" % webqtlConfig.PUBLICTHRESH)
-		results = map(lambda X:X[0], self.cursor.fetchall())
-		allRISets = filter(lambda X:X in results, allRISets)
-			
-		specMenuSub1 = HT.Optgroup(label = 'MOUSE')
-		specMenuSub2 = HT.Optgroup(label = 'RAT')
-		specMenuSub3 = HT.Optgroup(label = 'ARABIDOPSIS')
-		specMenuSub4 = HT.Optgroup(label = 'BARLEY')
-		for item in allRISets:
-			if item == 'HXBBXH':
-				specMenuSub2.append(('HXB/BXH', 'HXBBXH'))
-			elif item in ('BayXSha', 'ColXCvi', 'ColXBur'):
-				specMenuSub3.append((item, item))
-			elif item in ('SXM'):
-				specMenuSub4.append((item, item))
-			elif item == 'AXBXA':
-				specMenuSub1.append(('AXB/BXA', 'AXBXA'))
-			else:
-				specMenuSub1.append(tuple([item,item]))
-		crossMenu.append(specMenuSub1)
-		crossMenu.append(specMenuSub2)
-		crossMenu.append(specMenuSub3)
-		crossMenu.append(specMenuSub4)
-		crossMenu.selected.append('BXD')
-		crossMenuText = HT.Paragraph('Select the cross or recombinant inbred \
-		    set from the menu below. If you wish, paste data or select a data \
-		    file in the next sections')
- 		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(HT.Strong("From a File: "))
-		Para1.append('You can enter data by entering a file name here. The file\
-		    should contain a series of numbers representing trait values. The \
-		    values can be on one line separated by spaces or tabs, or they can \
-		    be on separate lines. Include one value for each progeny individual\
-		    or recombinant inbred line. Represent missing values with a \
-		    non-numeric character such as "x". If you have chosen a recombinant\
-		    inbred set, when you submit your data will be displayed in a form \
-		    where you can confirm and/or edit them. If you enter a file name \
-		    here, any data that you paste into the next section will be ignored.')
-		
-		filebox = HT.Paragraph(HT.Input(type='file', name='traitfile', size=20))
-
-		OR = HT.Paragraph(HT.Center(HT.Font(HT.Strong('OR'),color="red")))
-		
-		Para2 = HT.Paragraph()
-		Para2.append(HT.Strong("By Pasting or Typing Multiple Values:"))
-		Para2.append('You can enter data by pasting a series of numbers \
-		    representing trait values into this area. The values can be on one\
-		    line separated by spaces or tabs, or they can be on separate lines.\
-		    Include one value for each progeny individual or recombinant inbred\
-		    line. Represent missing values with a non-numeric character such \
-		    as "x". If you have chosen a recombinant inbred set, when you submit\
-		    your data will be displayed in a form where you can confirm and/or\
-		    edit them. If you enter a file name in the previous section, any \
-		    data that you paste here will be ignored. Check ', 
-		    HT.Href(url="/RIsample.html", text="sample data", target="_blank", Class="normalsize"), 
-		    ' for the correct format.')
-		
-		pastebox = HT.Paragraph(HT.Textarea(name='traitpaste', cols=45, rows=6))
-		# 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,OR,Para2,pastebox)
-		STEP2.append(HT.TR(TD1,TD2),HT.TR(HT.TD(colspan=2,height=20)))
-		
-		#############################
-		title3 = HT.Paragraph("&nbsp;&nbsp;3. Options:")
-		title3.__setattr__("class","subtitle")
-
-		STEP3 = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0)
-		
-		########
-		opt1 = HT.Paragraph(HT.Strong('Enable Use of Trait Variance: '))
-		opt1.append(HT.Input(type='checkbox', Class='checkbox', name=\
-		    'enablevariance', value='ON', onClick='xchange()'))
-		opt1.append(HT.BR(),'You may use your trait variance data in WebQTL,\
-		    if you check this box, you will be asked to submit your trait \
-		    variance data later')
-		
-		########
-		opt2 = HT.Paragraph(HT.Strong('Enable Use of Parents/F1: '))
-		opt2.append(HT.Input(type='checkbox', name='parentsf1', value='ON'))
-		opt2.append(HT.BR(),'Check this box if you wish to use Parents and F1 \
-		    data in WebQTL')
-		
-		########
-		opt3 = HT.Paragraph(HT.Strong("Name Your Trait ",HT.Font("(optional) ",\
-		    color="red")))
-		opt3.append(HT.Input(name='identification', size=12, maxlength=30))
-		# NL, 07/27/2010. variable 'IMGSTEP3' has been moved from templatePage.py to webqtlUtil.py;
-		TD1 = HT.TD(webqtlUtil.IMGSTEP3,width=58)
-		TD2 = HT.TD()
-		TD2.append(opt1,opt3)
-		STEP3.append(HT.TR(TD1,TD2),HT.TR(HT.TD(colspan=2,height=20)))
-		
-		#########################################
-		hddn = {'FormID':'crossChoice','submitID':'next', 'incparentsf1':'yes'}
-		
-		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=\
-		    'showNext(this.form);', Class="button") 			
-		reset = HT.Input(type='reset' ,name='reset' ,value='Reset',Class="button")
-		
-		sample = HT.Input(type='button' ,name='sample' ,value='Sample Data', \
-			onClick='showSample(this.form);',Class="button")
-		# NL, 07/27/2010. variable 'IMGNEXT' has been moved from templatePage.py to webqtlUtil.py;		
-		form.append(title1,HT.Center(STEP1,webqtlUtil.IMGNEXT),title2,HT.Center(STEP2,\
-		    webqtlUtil.IMGNEXT),title3,HT.Center(STEP3,webqtlUtil.IMGNEXT,HT.P(),submit,reset,sample))
-			
-		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)
-		
-