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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
#ODEPage.py
import string
from htmlgen import HTMLgen2 as HT
from base import webqtlConfig
from base.webqtlTrait import webqtlTrait
from base.templatePage import templatePage
from dbFunction import webqtlDatabaseFunction
class ODEPage(templatePage):
def __init__(self,fd):
templatePage.__init__(self, fd)
if not self.openMysql():
return
#XZ, self.theseTraits holds the "ProbeSet" traits.
self.theseTraits = []
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:
heading = 'ODE'
detail = ['You need to select at least one microarray trait to submit.']
self.error(heading=heading,detail=detail)
return
chipName = self.getChipName(fd)
species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
if species == 'rat':
species = 'Rattus norvegicus'
elif species == 'human':
species = 'Homo sapiens'
elif species == 'mouse':
species = 'Mus musculus'
else:
species = ''
probesetNameList = self.getProbesetNameList(fd)
TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee',valign="middle")
formODE = HT.Form(cgi="http://ontologicaldiscovery.org/index.php?action=manage&cmd=importGeneSet", enctype='multipart/form-data', name='formODE', submit = HT.Input(type='hidden'))
hddnODE = {}
hddnODE['client'] = 'genenetwork'
hddnODE['species'] = species
hddnODE['idtype'] = chipName
hddnODE['list'] = string.join(probesetNameList, ",")
for key in hddnODE.keys():
formODE.append(HT.Input(name=key, value=hddnODE[key], type='hidden'))
TD_LR.append(formODE)
TD_LR.append(HT.Paragraph("Your selections of %d traits is being exported to the ODE" % len(self.theseTraits), Class="cr fs16 fwb", align="Center"))
# updated by NL, moved mixedChipError() to webqtl.js and change it to mixedChipError(methodName)
if chipName == 'mixed':
methodName = "ODE"
self.dict['js1'] = """
<SCRIPT LANGUAGE="JavaScript">
setTimeout("mixedChipError('%s')",1000);
</SCRIPT>
""" % methodName
else:
self.dict['js1'] = """
<SCRIPT LANGUAGE="JavaScript">
setTimeout('document.formODE.submit()',1000);
</SCRIPT>
"""
self.dict['body'] = TD_LR
def getProbesetNameList(self, fd):
probesetNameList = []
for item in self.theseTraits:
probesetNameList.append(item.name)
return probesetNameList
def getChipName(self, fd):
chipName0 = ""
for item in self.theseTraits:
self.cursor.execute('SELECT GeneChip.Name FROM GeneChip, ProbeFreeze, ProbeSetFreeze WHERE GeneChip.Id = ProbeFreeze.ChipId and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.Name = "%s"' % item.db.name)
chipName = self.cursor.fetchone()[0]
if chipName != chipName0:
if chipName0:
return 'mixed'
else:
chipName0 = chipName
else:
pass
return chipName
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