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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)
+
+