Add all the source codes into the github.

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