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authorroot2012-05-08 18:39:56 -0500
committerroot2012-05-08 18:39:56 -0500
commitea46f42ee640928b92947bfb204c41a482d80937 (patch)
tree9b27a4eb852d12539b543c3efee9d2a47ef470f3 /web/webqtl/textUI/cmdClass.py
parent056b5253fc3857b0444382aa39944f6344dc1ceb (diff)
downloadgenenetwork2-ea46f42ee640928b92947bfb204c41a482d80937.tar.gz
Add all the source codes into the github.
Diffstat (limited to 'web/webqtl/textUI/cmdClass.py')
-rwxr-xr-xweb/webqtl/textUI/cmdClass.py224
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