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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
#GCATPage.py
from htmlgen import HTMLgen2 as HT
from base.webqtlTrait import webqtlTrait
from base.templatePage import templatePage
#Implemented by Xiaodong
class GCATPage(templatePage):
def __init__(self,fd):
self.theseTraits = []
TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee',valign="middle")
templatePage.__init__(self, fd)
if not self.openMysql():
return
self.searchResult = fd.formdata.getvalue('searchResult', [])
if type("1") == type(self.searchResult):
self.searchResult = [self.searchResult]
for item in self.searchResult:
try:
thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
thisTrait.retrieveInfo(QTL=1)
if thisTrait.db.type == "ProbeSet":
self.theseTraits.append(thisTrait)
except:
pass
if self.theseTraits:
pass
else:
templatePage.__init__(self, fd)
heading = 'GCAT'
detail = ['You need to select at least one microarray trait to submit to GCAT.']
self.error(heading=heading,detail=detail)
return
geneSymbolList = self.getGeneSymbolList()
geneSymbolSet = set(geneSymbolList)
if ( len(geneSymbolSet) < 500 ):
temp = '+'.join(geneSymbolSet)
GCATurl = "http://binf1.memphis.edu/gcat/?organism=mouse&subset=all&year=2010&geneInput=%s" % temp
self.dict['js1'] = """
<SCRIPT LANGUAGE="JavaScript">
setTimeout( 'window.location = "%s"', 2000 );
</SCRIPT>
""" % GCATurl
TD_LR.append(HT.Paragraph("Your selection of %d genes is being submitted to GCAT" % len(geneSymbolSet), Class="cr fs16 fwb", align="Center"))
else:
TD_LR.append(HT.Paragraph("Your selection of %d genes exceeds the limit of 500. Please reduce your gene number to below the limit." % len(geneSymbolSet), Class="cr fs16 fwb", align="Center"))
self.dict['body'] = TD_LR
def getGeneSymbolList(self):
geneList = []
for item in self.theseTraits:
item.retrieveInfo()
geneList.append(str(item.symbol))
return geneList
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