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Diffstat (limited to 'web/webqtl/submitTrait/CrossChoicePage.py')
| -rwxr-xr-x | web/webqtl/submitTrait/CrossChoicePage.py | 233 |
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(" 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(" 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(" 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) - - |