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