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Diffstat (limited to 'web/webqtl/submitTrait/VarianceChoicePage.py')
| -rwxr-xr-x | web/webqtl/submitTrait/VarianceChoicePage.py | 174 |
1 files changed, 0 insertions, 174 deletions
diff --git a/web/webqtl/submitTrait/VarianceChoicePage.py b/web/webqtl/submitTrait/VarianceChoicePage.py deleted file mode 100755 index bdbc47f9..00000000 --- a/web/webqtl/submitTrait/VarianceChoicePage.py +++ /dev/null @@ -1,174 +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 - -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(" 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(" 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) |