Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'

1 files changed, 0 insertions, 116 deletions

diff --git a/web/webqtl/heatmap/heatmapPage.py b/web/webqtl/heatmap/heatmapPage.py
deleted file mode 100755
index b407b0c8..00000000
--- a/web/webqtl/heatmap/heatmapPage.py
+++ /dev/null
@@ -1,116 +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
-
-import os
-import string
-from htmlgen import HTMLgen2 as HT
-
-from base.templatePage import templatePage
-from base import webqtlConfig
-from heatmap.Heatmap import Heatmap
-
-
-# XZ, 09/09/2008: After adding several traits to collection, click "QTL Heatmap" button,
-# XZ, 09/09/2008: This class will generate what you see.
-#########################################
-#      QTL heatmap Page
-#########################################
-class heatmapPage(templatePage):
-
-        def __init__(self,fd):
-
-                templatePage.__init__(self, fd)
-
-                if not self.openMysql():
-                        return
-                if not fd.genotype:
-                        fd.readGenotype()
-
-                searchResult = fd.formdata.getvalue('searchResult')
-                if not searchResult:
-                        heading = 'QTL Heatmap'
-                        detail = ['You need to select at least two traits in order to generate QTL heatmap.']
-                        self.error(heading=heading,detail=detail)
-                        return
-                if type("1") == type(searchResult):
-                        searchResult = string.split(searchResult,'\t')
-                if searchResult:
-                        if len(searchResult) > webqtlConfig.MAXCORR:
-                                heading = 'QTL Heatmap'
-                                detail = ['In order to display the QTL heat map properly, do not select more than %d traits for analysis.' % webqtlConfig.MAXCORR]
-                                self.error(heading=heading,detail=detail)
-                                return
-                else:
-                        heading = 'QTL Heatmap'
-                        detail = [HT.Font('Error : ',color='red'),HT.Font('Error occurs while retrieving data from database.',color='black')]
-                        self.error(heading=heading,detail=detail)
-                        return
-                self.dict['title'] = 'QTL heatmap'
-                NNN = len(searchResult)
-                if NNN == 0:
-                        heading = "QTL Heatmap"
-                        detail = ['No trait was selected for %s data set. No QTL heatmap was generated.' % fd.RISet]
-                        self.error(heading=heading,detail=detail)
-                        return
-                elif NNN < 2:
-                        heading = 'QTL Heatmap'
-                        detail = ['You need to select at least two traits in order to generate QTL heatmap.']
-                        self.error(heading=heading,detail=detail)
-                        return
-                else:
-                        colorScheme = fd.formdata.getvalue('colorScheme')
-                        if not colorScheme:
-                                colorScheme = '1'
-                        heatmapObject = Heatmap(fd=fd, searchResult=searchResult, colorScheme=colorScheme, userPrivilege=self.privilege, userName=self.userName)
-                        filename, areas, sessionfile = heatmapObject.getResult()
-                        gifmap = HT.Map(name='traitMap')
-                        for area in areas:
-                                Areas = HT.Area(shape='rect', coords=area[0], href=area[1], title=area[2])
-                                gifmap.areas.append(Areas)
-                        img2=HT.Image('/image/'+filename+'.png',border=0,usemap='#traitMap')
-                        imgUrl = 'Right-click or control-click on the link to download this graph as a <a href="/image/%s.png" class="normalsize" target="_blank">PNG file</a>' % filename
-                        form = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='showDatabase', submit=HT.Input(type='hidden'))
-                        hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_','RISet':fd.RISet,'searchResult':string.join(searchResult,'\t')}
-                        if fd.incparentsf1:
-                                hddn['incparentsf1']='ON'
-                        for key in hddn.keys():
-                                form.append(HT.Input(name=key, value=hddn[key], type='hidden'))
-                        heatmapButton = HT.Input(type='button' ,name='mintmap',value='Redraw QTL Heatmap', onClick="databaseFunc(this.form,'heatmap');",Class="button")
-                        spects = {'0':'Single Spectrum','1':'Grey + Blue + Red','2':'Blue + Red'}
-                        schemeMenu = HT.Select(name='colorScheme')
-                        schemeMenu.append(('Single Spectrum',0))
-                        schemeMenu.append(('Grey + Blue + Red',1))
-                        schemeMenu.append(('Blue + Red',2))
-                        schemeMenu.selected.append(spects[colorScheme])
-                        clusterCheck= HT.Input(type='checkbox', Class='checkbox', name='clusterCheck',checked=0)
-                        targetDescriptionCheck = HT.Input(type='checkbox', Class='checkbox', name='targetDescriptionCheck',checked=0)
-                        form.append(gifmap,schemeMenu, heatmapButton, HT.P(), clusterCheck, '  Cluster traits  ', targetDescriptionCheck, '  Add description', HT.P(),img2, HT.P(), imgUrl)
-                        form.append(HT.Input(name='session', value=sessionfile, type='hidden'))
-                        heatmapHelp = HT.Input(type='button' ,name='heatmapHelpButton',value='Info', onClick="openNewWin('/heatmap.html');",Class="button")
-                        heatmapHeading = HT.Paragraph('QTL Heatmap ', heatmapHelp, Class="title")
-                        TD_LR = HT.TD(colspan=2,height=200,width="100%",bgColor='#eeeeee')
-                        TD_LR.append(heatmapHeading, HT.P(),HT.P(),HT.P(),HT.P(),HT.P(),form)
-                        self.dict['body'] = str(TD_LR)