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-rwxr-xr-xweb/webqtl/textUI/cmdClass.py224
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
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 23:50:15 +0000