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authorroot2012-05-08 18:39:56 -0500
committerroot2012-05-08 18:39:56 -0500
commitea46f42ee640928b92947bfb204c41a482d80937 (patch)
tree9b27a4eb852d12539b543c3efee9d2a47ef470f3 /web/webqtl/submitTrait/VarianceChoicePage.py
parent056b5253fc3857b0444382aa39944f6344dc1ceb (diff)
downloadgenenetwork2-ea46f42ee640928b92947bfb204c41a482d80937.tar.gz
Add all the source codes into the github.
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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("&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)