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Diffstat (limited to 'web/webqtl/submitTrait/CrossChoicePage.py')
| -rwxr-xr-x | web/webqtl/submitTrait/CrossChoicePage.py | 233 |
1 files changed, 233 insertions, 0 deletions
diff --git a/web/webqtl/submitTrait/CrossChoicePage.py b/web/webqtl/submitTrait/CrossChoicePage.py new file mode 100755 index 00000000..fd919e5b --- /dev/null +++ b/web/webqtl/submitTrait/CrossChoicePage.py @@ -0,0 +1,233 @@ +# 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) + + |