diff options
Diffstat (limited to 'web/webqtl/textUI/cmdClass.py')
| -rwxr-xr-x | web/webqtl/textUI/cmdClass.py | 224 |
1 files changed, 224 insertions, 0 deletions
diff --git a/web/webqtl/textUI/cmdClass.py b/web/webqtl/textUI/cmdClass.py new file mode 100755 index 00000000..e394218e --- /dev/null +++ b/web/webqtl/textUI/cmdClass.py @@ -0,0 +1,224 @@ +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 |