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