def __init__(self, fd, traitInfos = None):
self.fd = fd
# This sets self.cursor
assert self.openMysql(), "No database"
# When is traitInfos used?
if traitInfos:
database, ProbeSetID, CellID = traitInfos
else:
print("fd is:", fd)
database = fd['database']
ProbeSetID = fd['ProbeSetID']
CellID = fd.get('CellID')
thisTrait = webqtlTrait(db=database, name=ProbeSetID, cellid=CellID, cursor=self.cursor)
if thisTrait.db.type == "ProbeSet":
self.cursor.execute('''SELECT Id, Name, FullName, confidentiality, AuthorisedUsers
FROM ProbeSetFreeze WHERE Name = "%s"''' % database)
indId, indName, indFullName, confidential, AuthorisedUsers = self.cursor.fetchall()[0]
if confidential == 1:
access_to_confidential_dataset = 0
#for the dataset that confidentiality is 1
#1. 'admin' and 'root' can see all of the dataset
#2. 'user' can see the dataset that AuthorisedUsers contains his id(stored in the Id field of User table)
if webqtlConfig.USERDICT[self.privilege] > webqtlConfig.USERDICT['user']:
access_to_confidential_dataset = 1
else:
AuthorisedUsersList=AuthorisedUsers.split(',')
if AuthorisedUsersList.__contains__(self.userName):
access_to_confidential_dataset = 1
if not access_to_confidential_dataset:
#Error, Confidential Database
heading = "Show Database"
detail = ["The %s database you selected is not open to the public \
at this time, please go back and select other database." % indFullName]
self.error(heading=heading,detail=detail,error="Confidential Database")
return
print("environ:", request.environ)
# Becuase of proxying remote_addr is probably localhost, so we first try for
# HTTP_X_FORWARDED_FOR
user_ip = request.environ.get('HTTP_X_FORWARDED_FOR') or request.remote_addr # in old app was fd.remote_ip
print("user_ip is:", user_ip)
query = "SELECT count(id) FROM AccessLog WHERE ip_address = %s and \
UNIX_TIMESTAMP()-UNIX_TIMESTAMP(accesstime)<86400"
self.cursor.execute(query,user_ip)
daycount = self.cursor.fetchall()
if daycount:
daycount = daycount[0][0]
if daycount > webqtlConfig.DAILYMAXIMUM:
heading = "Retrieve Data"
detail = ['For security reasons, the maximum access to a database is \
%d times per day per ip address. You have reached the limit, please \
try it again tomorrow.' % webqtlConfig.DAILYMAXIMUM]
self.error(heading=heading,detail=detail)
return
if thisTrait.db.type != 'ProbeSet' and thisTrait.cellid:
heading = "Retrieve Data"
detail = ['The Record you requested doesn\'t exist!']
self.error(heading=heading,detail=detail)
return
##identification, etc.
fd.identification = '%s : %s' % (thisTrait.db.shortname,ProbeSetID)
thisTrait.returnURL = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + '?FormID=showDatabase&database=%s\
&ProbeSetID=%s&RISet=%s&parentsf1=on' %(database, ProbeSetID, fd['RISet'])
if CellID:
fd.identification = '%s/%s'%(fd.identification, CellID)
thisTrait.returnURL = '%s&CellID=%s' % (thisTrait.returnURL, CellID)
thisTrait.retrieveInfo()
thisTrait.retrieveData()
self.updMysql()
self.cursor.execute("insert into AccessLog(accesstime,ip_address) values(Now(),%s)", user_ip)
self.openMysql()
##read genotype file
fd.RISet = thisTrait.riset
fd.readGenotype()
#if webqtlUtil.ListNotNull(map(lambda x:x.var, thisTrait.data.values())):
if any([x.variance for x in thisTrait.data.values()]):
fd.display_variance = True
fd.formID = 'varianceChoice'
DataEditingPage.__init__(self, fd, thisTrait)
def __init__(self, fd, traitInfos = []):
templatePage.__init__(self, fd)
if not self.openMysql():
return
TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee')
if traitInfos:
database,ProbeSetID,CellID = traitInfos
else:
database = fd.formdata.getfirst('database')
ProbeSetID = fd.formdata.getfirst('ProbeSetID')
CellID = fd.formdata.getfirst('CellID')
try:
thisTrait = webqtlTrait(db=database, name=ProbeSetID, cellid= CellID, cursor=self.cursor)
except:
heading = "Trait Data and Analysis Form"
detail = ["The trait isn't available currently."]
self.error(heading=heading,detail=detail,error="Error")
return
if thisTrait.db.type == "ProbeSet":
self.cursor.execute('''SELECT Id, Name, FullName, confidentiality, AuthorisedUsers
FROM ProbeSetFreeze WHERE Name = "%s"''' % database)
indId, indName, indFullName, confidential, AuthorisedUsers = self.cursor.fetchall()[0]
if confidential == 1:
access_to_confidential_dataset = 0
#for the dataset that confidentiality is 1
#1. 'admin' and 'root' can see all of the dataset
#2. 'user' can see the dataset that AuthorisedUsers contains his id(stored in the Id field of User table)
if webqtlConfig.USERDICT[self.privilege] > webqtlConfig.USERDICT['user']:
access_to_confidential_dataset = 1
else:
AuthorisedUsersList=AuthorisedUsers.split(',')
if AuthorisedUsersList.__contains__(self.userName):
access_to_confidential_dataset = 1
if not access_to_confidential_dataset:
#Error, Confidential Database
heading = "Show Database"
detail = ["The %s database you selected is not open to the public \
at this time, please go back and select other database." % indFullName]
self.error(heading=heading,detail=detail,error="Confidential Database")
return
user_ip = fd.remote_ip
query = "SELECT count(id) FROM AccessLog WHERE ip_address = %s and \
UNIX_TIMESTAMP()-UNIX_TIMESTAMP(accesstime)<86400"
self.cursor.execute(query,user_ip)
daycount = self.cursor.fetchall()
if daycount:
daycount = daycount[0][0]
if daycount > webqtlConfig.DAILYMAXIMUM:
heading = "Retrieve Data"
detail = ['For security reasons, the maximum access to a database is \
%d times per day per ip address. You have reached the limit, please \
try it again tomorrow.' % webqtlConfig.DAILYMAXIMUM]
self.error(heading=heading,detail=detail)
return
else:
pass
else:
pass
if thisTrait.db.type != 'ProbeSet' and thisTrait.cellid:
heading = "Retrieve Data"
detail = ['The Record you requested doesn\'t exist!']
self.error(heading=heading,detail=detail)
return
#XZ: Aug 23, 2010: I commented out this block because this feature is not used anymore
# check if animal information are available
"""
self.cursor.execute('''
SELECT
SampleXRef.ProbeFreezeId
FROM
SampleXRef, ProbeSetFreeze
WHERE
SampleXRef.ProbeFreezeId = ProbeSetFreeze.ProbeFreezeId AND
ProbeSetFreeze.Name = "%s"
''' % thisTrait.db.name)
sampleId = self.cursor.fetchall()
if sampleId:
thisTrait.strainInfo = 1
else:
thisTrait.strainInfo = None
"""
##identification, etc.
fd.identification = '%s : %s'%(thisTrait.db.shortname,ProbeSetID)
thisTrait.returnURL = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + '?FormID=showDatabase&database=%s\
&ProbeSetID=%s&RISet=%s&parentsf1=on' %(database,ProbeSetID,fd.RISet)
if CellID:
fd.identification = '%s/%s'%(fd.identification, CellID)
thisTrait.returnURL = '%s&CellID=%s' % (thisTrait.returnURL, CellID)
#retrieve trait information
try:
thisTrait.retrieveInfo()
thisTrait.retrieveData()
self.updMysql()
self.cursor.execute("insert into AccessLog(accesstime,ip_address) values(Now(),%s)" ,user_ip)
self.openMysql()
except:
heading = "Retrieve Data"
detail = ["The information you requested is not avaiable at this time."]
self.error(heading=heading,detail=detail)
return
##read genotype file
fd.RISet = thisTrait.riset
fd.readGenotype()
if webqtlUtil.ListNotNull(map(lambda x:x.var, thisTrait.data.values())):
fd.displayVariance = 1
fd.varianceDispName = 'SE'
fd.formID = 'varianceChoice'
self.dict['body']= thisTrait
DataEditingPage.__init__(self, fd, thisTrait)
self.dict['title'] = '%s: Display Trait' % fd.identification
def __init__(self, fd, traitInfos=None):
self.fd = fd
# This sets self.cursor
assert self.openMysql(), "No database"
# When is traitInfos used?
if traitInfos:
database, ProbeSetID, CellID = traitInfos
else:
print("fd is:", fd)
database = fd['database']
ProbeSetID = fd['ProbeSetID']
CellID = fd.get('CellID')
thisTrait = webqtlTrait(db=database,
name=ProbeSetID,
cellid=CellID,
cursor=self.cursor)
if thisTrait.db.type == "ProbeSet":
self.cursor.execute(
'''SELECT Id, Name, FullName, confidentiality, AuthorisedUsers
FROM ProbeSetFreeze WHERE Name = "%s"''' %
database)
indId, indName, indFullName, confidential, AuthorisedUsers = self.cursor.fetchall(
)[0]
if confidential == 1:
access_to_confidential_dataset = 0
#for the dataset that confidentiality is 1
#1. 'admin' and 'root' can see all of the dataset
#2. 'user' can see the dataset that AuthorisedUsers contains his id(stored in the Id field of User table)
if webqtlConfig.USERDICT[
self.privilege] > webqtlConfig.USERDICT['user']:
access_to_confidential_dataset = 1
else:
AuthorisedUsersList = AuthorisedUsers.split(',')
if AuthorisedUsersList.__contains__(self.userName):
access_to_confidential_dataset = 1
if not access_to_confidential_dataset:
#Error, Confidential Database
heading = "Show Database"
detail = [
"The %s database you selected is not open to the public \
at this time, please go back and select other database." %
indFullName
]
self.error(heading=heading,
detail=detail,
error="Confidential Database")
return
print("environ:", request.environ)
# Becuase of proxying remote_addr is probably localhost, so we first try for
# HTTP_X_FORWARDED_FOR
user_ip = request.environ.get(
'HTTP_X_FORWARDED_FOR'
) or request.remote_addr # in old app was fd.remote_ip
print("user_ip is:", user_ip)
query = "SELECT count(id) FROM AccessLog WHERE ip_address = %s and \
UNIX_TIMESTAMP()-UNIX_TIMESTAMP(accesstime)<86400"
self.cursor.execute(query, user_ip)
daycount = self.cursor.fetchall()
if daycount:
daycount = daycount[0][0]
if daycount > webqtlConfig.DAILYMAXIMUM:
heading = "Retrieve Data"
detail = [
'For security reasons, the maximum access to a database is \
%d times per day per ip address. You have reached the limit, please \
try it again tomorrow.' % webqtlConfig.DAILYMAXIMUM
]
self.error(heading=heading, detail=detail)
return
if thisTrait.db.type != 'ProbeSet' and thisTrait.cellid:
heading = "Retrieve Data"
detail = ['The Record you requested doesn\'t exist!']
self.error(heading=heading, detail=detail)
return
##identification, etc.
fd.identification = '%s : %s' % (thisTrait.db.shortname, ProbeSetID)
thisTrait.returnURL = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + '?FormID=showDatabase&database=%s\
&ProbeSetID=%s&RISet=%s&parentsf1=on' % (database, ProbeSetID,
fd['RISet'])
if CellID:
fd.identification = '%s/%s' % (fd.identification, CellID)
thisTrait.returnURL = '%s&CellID=%s' % (thisTrait.returnURL,
CellID)
thisTrait.retrieveInfo()
thisTrait.retrieveData()
self.updMysql()
self.cursor.execute(
"insert into AccessLog(accesstime,ip_address) values(Now(),%s)",
user_ip)
self.openMysql()
##read genotype file
fd.RISet = thisTrait.riset
fd.readGenotype()
#if webqtlUtil.ListNotNull(map(lambda x:x.var, thisTrait.data.values())):
if any([x.variance for x in thisTrait.data.values()]):
fd.display_variance = True
fd.formID = 'varianceChoice'
DataEditingPage.__init__(self, fd, thisTrait)
def __init__(self,fd):
########## geneName means symbol ##########
geneName = fd.formdata.getvalue('gene')
if geneName:
geneName = string.strip(geneName)
refseq = fd.formdata.getvalue('refseq')
if refseq:
refseq = string.strip(refseq)
genbankid = fd.formdata.getvalue('genbankid')
if genbankid:
genbankid = string.strip(genbankid)
geneid = fd.formdata.getvalue('geneid')
if geneid:
geneid = string.strip(geneid)
species = fd.formdata.getvalue('species')
tissue = fd.formdata.getvalue('tissue')
database = fd.formdata.getvalue('database')
########## searchAlias is just a singal, so it doesn't need be stripped ##########
searchAlias = fd.formdata.getvalue('searchAlias')
if not self.openMysql():
return
if database:
if geneName:
if searchAlias:
self.cursor.execute(""" SELECT ProbeSetXRef.*
FROM
ProbeSet, ProbeSetXRef, DBList
WHERE
ProbeSetXRef.ProbeSetFreezeId = DBList.FreezeId AND
ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
(DBList.Name=%s or DBList.Code=%s) AND
MATCH (ProbeSet.symbol, alias) AGAINST ("+%s" IN BOOLEAN MODE)
ORDER BY ProbeSetXRef.mean DESC
""" , (database, database, geneName))
else:
self.cursor.execute(""" SELECT ProbeSetXRef.*
FROM
ProbeSet, ProbeSetXRef, DBList
WHERE
ProbeSetXRef.ProbeSetFreezeId = DBList.FreezeId AND
ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
(DBList.Name=%s or DBList.Code=%s) AND
ProbeSet.symbol = %s
ORDER BY ProbeSetXRef.mean DESC
""" , (database, database, geneName))
elif refseq:
self.cursor.execute(""" SELECT ProbeSetXRef.*
FROM
ProbeSet, ProbeSetXRef, DBList
WHERE
ProbeSetXRef.ProbeSetFreezeId = DBList.FreezeId AND
ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
(DBList.Name=%s or DBList.Code=%s) AND
ProbeSet.RefSeq_TranscriptId = %s
ORDER BY ProbeSetXRef.mean DESC
""" , (database, database, refseq))
elif genbankid:
self.cursor.execute(""" SELECT ProbeSetXRef.*
FROM
ProbeSet, ProbeSetXRef, DBList
WHERE
ProbeSetXRef.ProbeSetFreezeId = DBList.FreezeId AND
ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
(DBList.Name=%s or DBList.Code=%s) AND
ProbeSet.GenbankId = %s
ORDER BY ProbeSetXRef.mean DESC
""" , (database, database, genbankid))
elif geneid:
self.cursor.execute(""" SELECT ProbeSetXRef.*
FROM
ProbeSet, ProbeSetXRef, DBList
WHERE
ProbeSetXRef.ProbeSetFreezeId = DBList.FreezeId AND
ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
(DBList.Name=%s or DBList.Code=%s) AND
ProbeSet.GeneId = %s
ORDER BY ProbeSetXRef.mean DESC
""" , (database, database, geneid))
Results = self.cursor.fetchone()
########## select the Data that match the selection(currently, only max mean available) ##########
if Results:
ProbeSetFreezeId = Results[0]
ProbeSetId = Results[1]
DataId = Results[2]
self.cursor.execute("""
select
InbredSet.Name
from
InbredSet, ProbeFreeze, ProbeSetFreeze
where
InbredSet.Id=ProbeFreeze.InbredSetId and
ProbeFreeze.Id=ProbeSetFreeze.ProbeFreezeId and
ProbeSetFreeze.Id=%s
""", ProbeSetFreezeId)
fd.RISet = self.cursor.fetchone()[0]
#fd.RISet = Results[0]
self.cursor.execute("select Name, FullName from ProbeSetFreeze where Id=%s", ProbeSetFreezeId)
fd.database, fd.identification = self.cursor.fetchone()
self.cursor.execute("select Name, symbol, description from ProbeSet where Id=%s", ProbeSetId)
fd.ProbeSetID, fd.symbol, fd.description = self.cursor.fetchone()
fd.identification += ' : '+fd.ProbeSetID
fd.formdata['fullname'] = fd.database+'::'+fd.ProbeSetID
#XZ, 03/03/2009: Xiaodong changed Data to ProbeSetData
self.cursor.execute("select Strain.Name, ProbeSetData.Value from Strain, ProbeSetData where Strain.Id=ProbeSetData.StrainId and ProbeSetData.Id=%s", DataId)
Results = self.cursor.fetchall()
fd.allstrainlist = []
for item in Results:
fd.formdata[item[0]] = item[1]
fd.allstrainlist.append(item[0])
#XZ, 03/12/2009: Xiaodong changed SE to ProbeSetSE
self.cursor.execute("select Strain.Name, ProbeSetSE.error from Strain, ProbeSetSE where Strain.Id = ProbeSetSE.StrainId and ProbeSetSE.DataId=%s", DataId)
Results = self.cursor.fetchall()
for item in Results:
fd.formdata['V'+item[0]] = item[1]
else:
fd.RISet = 'BXD'
fd.database = 'KI_2A_0405_Rz'
fd.ProbeSetID = '1367452_at'
else:
fd.RISet = 'BXD'
fd.database = 'KI_2A_0405_Rz'
fd.ProbeSetID = '1367452_at'
#BasicStatisticsPage.__init__(self, fd)
thisTrait = webqtlTrait(db=fd.database, name=fd.ProbeSetID, cursor=self.cursor)
thisTrait.retrieveInfo()
thisTrait.retrieveData()
DataEditingPage.__init__(self, fd, thisTrait)
self.dict['title'] = '%s: Display Trait' % fd.identification