Add all the source codes into the github.

1 files changed, 174 insertions, 0 deletions

diff --git a/web/webqtl/submitTrait/VarianceChoicePage.py b/web/webqtl/submitTrait/VarianceChoicePage.py
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+++ b/web/webqtl/submitTrait/VarianceChoicePage.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
+
+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)