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authorzsloan2015-03-27 20:28:51 +0000
committerzsloan2015-03-27 20:28:51 +0000
commitd0911a04958a04042da02a334ccc528dae79cc17 (patch)
tree3c48e2e937c1dbeaf00a5697c87ed251afa5c8f1 /web/webqtl/submitTrait/CrossChoicePage.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/CrossChoicePage.py')
-rwxr-xr-xweb/webqtl/submitTrait/CrossChoicePage.py233
1 files changed, 0 insertions, 233 deletions
diff --git a/web/webqtl/submitTrait/CrossChoicePage.py b/web/webqtl/submitTrait/CrossChoicePage.py
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--- a/web/webqtl/submitTrait/CrossChoicePage.py
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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
-
-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("&nbsp;&nbsp;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("&nbsp;&nbsp;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("&nbsp;&nbsp;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)
-
-