import string import os import MySQLdb from base import webqtlConfig ######################################### # Basic Class ######################################### class cmdClass: def __init__(self,fd): self.contents = [] self.accessError = 0 self.error = 0 self.accessCode = '###Database Code : <a href="%s%s?cmd=help">%s%s?cmd=help</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE) self.data = fd.formdata self.cmdID = self.data.getvalue('cmd') self.showurl = self.data.getvalue('url') self.cursor = None self.user_ip = fd.remote_ip try: if not self.openMysql(): self.accessError = 1 self.contents = ['###Error: Database is not ready'] return if not self.accessCount(): self.accessError = 1 self.contents = ['###Error: You have reached maximum access today '] return self.accessRecord() except: self.accessError = 1 self.contents = ['###Error: Database is not ready'] return self.probeset = self.data.getvalue('probeset') self.database = self.data.getvalue('db') self.probe = self.data.getvalue('probe') self.sourcedata = [] try: self.format = self.data.getvalue('format')[:3] except: self.format = 'row' if not self.probeset or not self.database: self.error = 1 return def openMysql(self): try: # con = MySQLdb.Connect(db='db_webqtl', host = webqtlConfig.MYSQL_SERVER) # Modified by Fan Zhang con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD) self.cursor = con.cursor() return 1 except: return 0 #XZ, 03/23/2009: The function name is confusing. This function is to get the database type(ProbeSet, Publish, Geno) id. def getDBId(self,code): self.cursor.execute('SELECT DBType.Name, DBList.FreezeId from DBType, DBList WHERE DBType.Id = DBList.DBTypeId and DBList.code= "%s"' % code) result = self.cursor.fetchall() if not result: return (None, None) else: return result[0] #XZ, 03/23/2009: This is to get the inbredset name. def getRISet(self,prefix, DbId): if prefix == 'ProbeSet': self.cursor.execute('SELECT InbredSet.Name from InbredSet, ProbeSetFreeze, ProbeFreeze WHERE ProbeFreeze.InbredSetId = InbredSet.Id and ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId and ProbeSetFreeze.Id = %d' % DbId) else: self.cursor.execute('SELECT InbredSet.Name from %sFreeze, InbredSet WHERE %sFreeze.InbredSetId = InbredSet.Id and %sFreeze.Id = %d' % (prefix, prefix, prefix, DbId)) result = self.cursor.fetchall() if result: if result[0][0] == "BXD300": return "BXD" else: return result[0][0] else: return None def accessCount(self): try: user_ip = self.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: return 0 else: return 1 else: return 1 except: return 0 def accessRecord(self): try: user_ip = self.user_ip self.updMysql() query = """INSERT INTO AccessLog(accesstime,ip_address) values(Now(),%s)""" self.cursor.execute(query,user_ip) self.openMysql() except: pass def __str__(self): text = map(str,self.contents) if self.showurl: text.append('http://%s%s?%s' % (os.environ['HTTP_HOST'],os.environ['SCRIPT_NAME'],os.environ['QUERY_STRING'][:-8])) text += self.sourcedata return string.join(text,'\n') def write(self): if self.cursor: self.cursor.close() try: browser = os.environ['HTTP_USER_AGENT'] return '<pre>%s</pre>' % str(self) except: return str(self) def write2(self): print str(self) def getTraitData(self, prefix, dbId, probeset, probe = None): headerDict = {'ProbeSet':'ProbeSetID', 'Publish':'RecordID', 'Geno':'Locus'} if prefix == None or dbId == None: return None, None if probe and prefix=='ProbeSet': #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=get&probeset=98332_at&db=bra08-03MAS5&probe=pm&format=col if string.lower(probe) in ("all","mm","pm"): query = "SELECT Probe.Name from Probe, ProbeSet WHERE Probe.ProbeSetId = ProbeSet.Id and ProbeSet.Name = '%s' order by Probe.Name" % probeset self.cursor.execute(query) allprobes = self.cursor.fetchall() if not allprobes: return None, None fetchprobes = [] for item in allprobes: if probe == 'all': fetchprobes.append(item[0]) else: try: taildigit = int(item[0][-1]) % 2 if probe == "pm" and taildigit == 1: fetchprobes.append(item[0]) if probe == "mm" and taildigit == 0: fetchprobes.append(item[0]) except: pass if not fetchprobes: return None, None #XZ, 03/05/2009: Xiaodong changed Data to ProbeData query = "SELECT Strain.Name, ProbeData.value, Probe.Name from ProbeData, ProbeFreeze, ProbeSetFreeze, ProbeXRef, Strain, Probe, ProbeSet WHERE ProbeSet.Name = '%s' and Probe.ProbeSetId = ProbeSet.Id and ProbeXRef.ProbeId = Probe.Id and ProbeXRef.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.Id = %d and ProbeXRef.DataId = ProbeData.Id and ProbeData.StrainId = Strain.Id and Probe.Name in (%s) order by Strain.Id, Probe.Name " % (probeset,dbId, "'" + string.join(fetchprobes, "', '") +"'") self.cursor.execute(query) traitdata = self.cursor.fetchall() if not traitdata: pass else: nfield = len(fetchprobes) heads = [['ProbeSet'] + [probeset]*nfield] heads.append(['probe'] + fetchprobes) posdict = {} i = 0 for item in fetchprobes: posdict[item] = i i += 1 prevStrain = '' traitdata2 = [] i = -1 for item in traitdata: if item[0] != prevStrain: prevStrain = item[0] i += 1 traitdata2.append([item[0]] + [None] * nfield) else: pass traitdata2[i][posdict[item[-1]]+1] = item[1] traitdata = traitdata2 #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=get&probeset=98332_at&db=bra08-03MAS5&probe=119637&format=col else: heads = [('ProbeSetId', probeset), ('ProbeId',probe)] #XZ, 03/05/2009: Xiaodong changed Data to ProbeData query = "SELECT Strain.Name, ProbeData.value from ProbeData, ProbeFreeze, ProbeSetFreeze, ProbeXRef, Strain, Probe, ProbeSet WHERE Probe.Name = '%s' and ProbeSet.Name = '%s' and Probe.ProbeSetId = ProbeSet.Id and ProbeXRef.ProbeId = Probe.Id and ProbeXRef.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.Id = %d and ProbeXRef.DataId = ProbeData.Id and ProbeData.StrainId = Strain.Id" % (probe,probeset,dbId) #print 'Content-type: text/html\n' self.cursor.execute(query) traitdata = self.cursor.fetchall() #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=get&probeset=98332_at&db=bra08-03MAS5&format=col elif prefix=='ProbeSet': #XZ: probeset data heads = [(headerDict[prefix], probeset)] query = "SELECT Strain.Name, %sData.value from %sData, Strain, %s, %sXRef WHERE %s.Name = '%s' and %sXRef.%sId = %s.Id and %sXRef.%sFreezeId = %d and %sXRef.DataId = %sData.Id and %sData.StrainId = Strain.Id order by Strain.Id" % (prefix, prefix, prefix, prefix, prefix, probeset,prefix, prefix, prefix, prefix, prefix, dbId, prefix, prefix, prefix) self.cursor.execute(query) traitdata = self.cursor.fetchall() #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=get&probeset=10834&db=BXDPublish&format=col elif prefix=='Publish': heads = [(headerDict[prefix], probeset)] #XZ, 03/05/2009: Xiaodong changed Data to PublishData query = "SELECT Strain.Name, PublishData.value from PublishData, Strain, PublishXRef, PublishFreeze WHERE PublishXRef.InbredSetId = PublishFreeze.InbredSetId and PublishData.Id = PublishXRef.DataId and PublishXRef.Id = %s and PublishFreeze.Id = %d and PublishData.StrainId = Strain.Id" % (probeset, dbId) self.cursor.execute(query) traitdata = self.cursor.fetchall() #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=get&probeset=rs13475701&db=BXDGeno&format=col else: #XZ: genotype data heads = [(headerDict[prefix], probeset)] RISet = self.getRISet(prefix, dbId) self.cursor.execute("select SpeciesId from InbredSet where Name = '%s'" % RISet) speciesId = self.cursor.fetchone()[0] #XZ, 03/05/2009: Xiaodong changed Data to %sData query = "SELECT Strain.Name, %sData.value from %sData, Strain, %s, %sXRef WHERE %s.SpeciesId=%s and %s.Name = '%s' and %sXRef.%sId = %s.Id and %sXRef.%sFreezeId = %d and %sXRef.DataId = %sData.Id and %sData.StrainId = Strain.Id order by Strain.Id" % (prefix, prefix, prefix, prefix, prefix, speciesId, prefix, probeset,prefix, prefix, prefix, prefix, prefix, dbId, prefix, prefix, prefix) self.cursor.execute(query) traitdata = self.cursor.fetchall() if traitdata: return traitdata, heads else: return None, None