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)
def exportDatasetPage(self, fd, PublishFreeze_Name):
#return PublishFreeze_Name
if not self.openMysql():
return
self.cursor.execute( "select InbredSet.Name from PublishFreeze, InbredSet where PublishFreeze.InbredSetId=InbredSet.Id and PublishFreeze.Name='%s'" % PublishFreeze_Name )
self.RISet = self.cursor.fetchone()[0]
fd.RISet = self.RISet
fd.incparentsf1 = 1
fd.readGenotype()
strainlist = fd.f1list + fd.strainlist
#return str(strainlist)
self.cursor.execute("Select Species.Name from Species, InbredSet where InbredSet.SpeciesId = Species.Id and InbredSet.Name = '%s'" % fd.RISet)
self.Species = self.cursor.fetchone()[0]
#return Species
self.searchResult = []
self.cursor.execute("Select PublishXRef.Id from PublishXRef, InbredSet where PublishXRef.InbredSetId = InbredSet.Id and InbredSet.Name = '%s'" % self.RISet)
result = self.cursor.fetchall()
for one_result in result:
self.searchResult.append( "%s::%s" % (PublishFreeze_Name, one_result[0]) )
#return self.searchResult
fields = ["ID", "Species", "Cross", "Database", "ProbeSetID / RecordID", "Symbol", "Description", "ProbeTarget", "PubMed_ID", "Phenotype", "Chr", "Mb", "Alias", "Gene_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", "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
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.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], thisTrait.locus, thisTrait.lrs, thisTrait.pvalue])
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.unigeneid, "", "", "", "", "", "", "", "", "", ""])
elif thisTrait.db.type == 'Publish':
if thisTrait.pre_publication_description:
if thisTrait.pubmed_id:
text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name, "", "", "", thisTrait.pubmed_id, thisTrait.post_publication_description, "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""])
else:
text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name, "", "", "", "", thisTrait.pre_publication_description, "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""])
else:
text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name, "", "", "", thisTrait.pubmed_id, thisTrait.post_publication_description, "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""])
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:
mean = 'N/A'
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
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)
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)
