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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
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)
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