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authorzsloan2015-03-27 20:28:51 +0000
committerzsloan2015-03-27 20:28:51 +0000
commitd0911a04958a04042da02a334ccc528dae79cc17 (patch)
tree3c48e2e937c1dbeaf00a5697c87ed251afa5c8f1 /web/webqtl/submitTrait/VarianceChoicePage.py
parenta840ad18e1fe3db98a359a159e9b9b72367a2839 (diff)
downloadgenenetwork2-d0911a04958a04042da02a334ccc528dae79cc17.tar.gz
Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'
Diffstat (limited to 'web/webqtl/submitTrait/VarianceChoicePage.py')
-rwxr-xr-xweb/webqtl/submitTrait/VarianceChoicePage.py174
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("&nbsp;&nbsp;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("&nbsp;&nbsp;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)