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

1 files changed, 0 insertions, 174 deletions

diff --git a/web/webqtl/submitTrait/VarianceChoicePage.py b/web/webqtl/submitTrait/VarianceChoicePage.py
deleted file mode 100755
index bdbc47f9..00000000
--- a/web/webqtl/submitTrait/VarianceChoicePage.py
+++ /dev/null
@@ -1,174 +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
-
-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 "Enter Trait Data".
-# XZ, 09/09/2008: If user check "Enable Use of Trait Variance",
-# XZ, 09/09/2008: this class generate what you see
-#########################################
-#      VarianceChoicePage
-#########################################
-
-class VarianceChoicePage(templatePage):
-
-	def __init__(self, fd):
-
-		templatePage.__init__(self, fd)
-
-		self.dict['title'] = 'Variance Submission' 
-		
-		if not fd.genotype:
-			fd.readData(incf1=1)
-		
-		TD_LEFT = """
-		<TD vAlign=top width="45%" bgColor=#eeeeee>
-			<P class="title">Introduction</P>
-			<BLOCKQUOTE>
-				<P>The variance 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 target="_blank" Href=\
-				"RIsample.html" 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(" Variance Submission Form")
-		main_title.__setattr__("class","title")
-
-		#############################
-		title2 = HT.Paragraph("&nbsp;&nbsp;1. Enter variance 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 variance 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='variancefile', 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 variance 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.')
-		
-		pastebox = HT.Paragraph(HT.Textarea(name='variancepaste', cols=45, rows=6))
-		# 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(Para1,filebox,OR,Para2,pastebox)
-		STEP2.append(HT.TR(TD1,TD2),HT.TR(HT.TD(colspan=2,height=20)))
-		#########################################
-		
-		hddn = {'FormID':'varianceChoice','submitID':'next','RISet':fd.RISet}
-		if fd.identification:
-			hddn['identification'] = fd.identification
-		if fd.enablevariance:
-			hddn['enablevariance']='ON'
-		
-		if fd.incparentsf1:
-			hddn['incparentsf1']='ON'
-		
-		for item, value in fd.allTraitData.items():
-			if value.val:
-				hddn[item] = value.val
-		
-		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")
-		
-		#########################################
-		title3 = HT.Paragraph("&nbsp;&nbsp;2. Submit:")
-		title3.__setattr__("class","subtitle")
-
-		STEP3 = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0)
-		
-		# 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(HT.Blockquote("Click the next button to submit your variance\
-		data for editing and mapping."),HT.Center(submit,reset))
-		STEP3.append(HT.TR(TD1,TD2),HT.TR(HT.TD(colspan=2,height=20)))
-		
-		#########################################
-		
-		# NL, 07/27/2010. variable 'IMGNEXT' has been moved from templatePage.py to webqtlUtil.py;
-		form.append(title2,HT.Center(STEP2,webqtlUtil.IMGNEXT),title3,HT.Center(STEP3))
-			
-		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)