Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'

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