Add all the source codes into the github.

1 files changed, 233 insertions, 0 deletions

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