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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
#ExportSelectionDetailInfoPage.py
import string
from htmlgen import HTMLgen2 as HT
import os
import time
import pyXLWriter as xl
import reaper
from base import webqtlConfig
from base.templatePage import templatePage
from utility import webqtlUtil
from base.webqtlTrait import webqtlTrait
#########################################
# Export Selection DetailInfo Page
#########################################
class ExportSelectionDetailInfoPage(templatePage):
def __init__(self,fd):
templatePage.__init__(self, fd)
if not self.openMysql():
return
fd.incparentsf1 = 1
if not fd.genotype:
fd.readGenotype()
locusChr = {}
locusMb = {}
for chr in fd.genotype:
for locus in chr:
locusChr[locus.name] = locus.chr
locusMb[locus.name] = locus.Mb
self.searchResult = fd.formdata.getvalue('searchResult')
if not self.searchResult:
templatePage.__init__(self, fd)
heading = 'Export Collection'
detail = ['You need to select at least one trait to export.']
self.error(heading=heading,detail=detail)
return
self.RISet = fd.formdata.getvalue("RISet")
self.cursor.execute("Select Species.Name from Species, InbredSet where InbredSet.SpeciesId = Species.Id and InbredSet.Name = '%s'" % self.RISet)
self.Species = self.cursor.fetchone()[0]
if type("1") == type(self.searchResult):
self.searchResult = string.split(self.searchResult,'\t')
strainlist = fd.f1list + fd.strainlist
fields = ["ID", "Species", "Cross", "Database", "ProbeSetID / RecordID", "Symbol", "Description", "ProbeTarget", "PubMed_ID", "Phenotype", "Chr", "Mb", "Alias", "Gene_ID", "HomoloGene_ID", "UniGene_ID", "Strand_Probe ", "Strand_Gene ", "Probe_set_specificity", "Probe_set_BLAT_score", "Probe_set_BLAT_Mb_start", "Probe_set_BLAT_Mb_end ", "QTL_Chr", "QTL_Mb", "Locus_at_Peak", "Max_LRS", "P_value_of_MAX", "Mean_Expression"] + strainlist
if self.searchResult:
traitList = []
for item in self.searchResult:
thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
thisTrait.retrieveInfo(QTL=1)
thisTrait.retrieveData(strainlist=strainlist)
traitList.append(thisTrait)
text = [fields]
for i, thisTrait in enumerate(traitList):
if thisTrait.db.type == 'ProbeSet':
if not thisTrait.cellid: #ProbeSet
#12/22/2009, XZ: We calculated LRS for each marker(locus) in geno file and record the max LRS and its corresponding marker in MySQL database. But after the calculation, Rob deleted several markers. If one of the deleted markers happen to be the one recorded in database, error will occur. So we have to deal with this situation.
if locusChr.has_key(thisTrait.locus) and locusMb.has_key(thisTrait.locus):
text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name, thisTrait.symbol, thisTrait.description, thisTrait.probe_target_description,"", "", thisTrait.chr, thisTrait.mb, thisTrait.alias, thisTrait.geneid, thisTrait.homologeneid, thisTrait.unigeneid, thisTrait.strand_probe, thisTrait.strand_gene, thisTrait.probe_set_specificity, thisTrait.probe_set_blat_score, thisTrait.probe_set_blat_mb_start, thisTrait.probe_set_blat_mb_end, locusChr[thisTrait.locus], locusMb[thisTrait.locus], thisTrait.locus, thisTrait.lrs, thisTrait.pvalue])
else:
text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name, thisTrait.symbol, thisTrait.description, thisTrait.probe_target_description,"", "", thisTrait.chr, thisTrait.mb, thisTrait.alias, thisTrait.geneid, thisTrait.homologeneid, thisTrait.unigeneid, thisTrait.strand_probe, thisTrait.strand_gene, thisTrait.probe_set_specificity, thisTrait.probe_set_blat_score, thisTrait.probe_set_blat_mb_start, thisTrait.probe_set_blat_mb_end, "", "", "", "", ""])
else: #Probe
text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name + " : " + thisTrait.cellid, thisTrait.symbol, thisTrait.description, thisTrait.probe_target_description,"", "", thisTrait.chr, thisTrait.mb, thisTrait.alias, thisTrait.geneid, thisTrait.homologeneid, thisTrait.unigeneid, "", "", "", "", "", "", "", "", "", "", ""])
elif thisTrait.db.type == 'Publish':
#XZ: need to consider confidential phenotype
PhenotypeString = thisTrait.post_publication_description
if thisTrait.confidential:
if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=thisTrait.authorized_users):
PhenotypeString = thisTrait.pre_publication_description
text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name, "", "", "", thisTrait.pubmed_id, PhenotypeString, "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""])
elif thisTrait.db.type == 'Temp':
text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name, "", thisTrait.description, "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "","", ""])
elif thisTrait.db.type == 'Geno':
text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name, "", thisTrait.name,"", "", "", thisTrait.chr, thisTrait.mb, "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""])
else:
continue
testval = thisTrait.exportData(strainlist)
try:
mean = reaper.anova(testval)[0]
except:
count = 0
sum = 0
for oneValue in testval:
try:
oneValue = float(oneValue)
sum = sum + oneValue
count = count + 1
except:
pass
if count == 0:
mean = 0
else:
mean = sum/count
text[-1].append(mean)
text[-1] += testval
if len(text[0]) < 255 or len(text) < 255:
transpose = 0
if len(text[0]) >= 255:
text = webqtlUtil.transpose(text)
transpose = 1
filename = os.path.join(webqtlConfig.TMPDIR, webqtlUtil.generate_session() +'.xls')
# Create a new Excel workbook
workbook = xl.Writer(filename)
worksheet = workbook.add_worksheet()
headingStyle = workbook.add_format(align = 'center', bold = 1, size=13, color = 'green')
titleStyle = workbook.add_format(align = 'left', bold = 0, size=13, border = 1, border_color="gray")
##Write title Info
# Modified by Hongqiang Li
# worksheet.write([0, 0], "Data source: The GeneNetwork at web2qtl.utmem.edu:88", titleStyle)
# worksheet.write([1, 0], "Citations: Please see web2qtl.utmem.edu:88/reference.html", titleStyle)
worksheet.write([0, 0], "Data source: The GeneNetwork at %s" % webqtlConfig.PORTADDR, titleStyle)
worksheet.write([1, 0], "Citations: Please see %s/reference.html" % webqtlConfig.PORTADDR, titleStyle)
#
worksheet.write([2, 0], "Date : %s" % time.strftime("%B %d, %Y", time.gmtime()), titleStyle)
worksheet.write([3, 0], "Time : %s GMT" % time.strftime("%H:%M ", time.gmtime()), titleStyle)
# Modified by Hongqiang Li
# worksheet.write([4, 0], "Status of data ownership: Possibly unpublished data; please see web2qtl.utmem.edu:88/statusandContact.html for details on sources, ownership, and usage of these data.", titleStyle)
worksheet.write([4, 0], "Status of data ownership: Possibly unpublished data; please see %s/statusandContact.html for details on sources, ownership, and usage of these data." % webqtlConfig.PORTADDR, titleStyle)
#
worksheet.write([6, 0], "This output file contains data from %d GeneNetwork databases listed below" % len(traitList), titleStyle)
# Row and column are zero indexed
nrow = startRow = 8
for row in text:
for ncol, cell in enumerate(row):
if nrow == startRow:
worksheet.write([nrow, ncol], cell.strip(), headingStyle)
worksheet.set_column([ncol, ncol], 2*len(cell))
else:
worksheet.write([nrow, ncol], cell)
nrow += 1
worksheet.write([nrow+1, 0], "Funding for The GeneNetwork: NIAAA (U01AA13499, U24AA13513), NIDA, NIMH, and NIAAA (P20-DA 21131), NCI MMHCC (U01CA105417), and NCRR (U24 RR021760)", titleStyle)
worksheet.write([nrow+2, 0], "PLEASE RETAIN DATA SOURCE INFORMATION WHENEVER POSSIBLE", titleStyle)
workbook.close()
fp = open(filename, 'rb')
text = fp.read()
fp.close()
self.content_type = 'application/xls'
self.content_disposition = 'attachment; filename=%s' % ('export-%s.xls' % time.strftime("%y-%m-%d-%H-%M"))
self.attachment = text
else:
self.content_type = 'application/xls'
self.content_disposition = 'attachment; filename=%s' % ('export-%s.txt' % time.strftime("%y-%m-%d-%H-%M"))
for item in text:
self.attachment += string.join(map(str, item), '\t')+ "\n"
self.cursor.close()
else:
fd.req.content_type = 'text/html'
heading = 'Export Collection'
detail = [HT.Font('Error : ',color='red'),HT.Font('Error occurs while retrieving data from database.',color='black')]
self.error(heading=heading,detail=detail)
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