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-rwxr-xr-xweb/webqtl/textUI/__init__.py0
-rwxr-xr-xweb/webqtl/textUI/cmdClass.py224
-rwxr-xr-xweb/webqtl/textUI/cmdCorrelation.py325
-rwxr-xr-xweb/webqtl/textUI/cmdGeno.py118
-rwxr-xr-xweb/webqtl/textUI/cmdGet.py86
-rwxr-xr-xweb/webqtl/textUI/cmdHelp.py105
-rwxr-xr-xweb/webqtl/textUI/cmdInterval.py174
-rwxr-xr-xweb/webqtl/textUI/cmdMap.py144
-rwxr-xr-xweb/webqtl/textUI/cmdSearchGene.py70
-rwxr-xr-xweb/webqtl/textUI/cmdShowEditing.py50
10 files changed, 0 insertions, 1296 deletions
diff --git a/web/webqtl/textUI/__init__.py b/web/webqtl/textUI/__init__.py
deleted file mode 100755
index e69de29b..00000000
--- a/web/webqtl/textUI/__init__.py
+++ /dev/null
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
diff --git a/web/webqtl/textUI/cmdCorrelation.py b/web/webqtl/textUI/cmdCorrelation.py
deleted file mode 100755
index 04595fc5..00000000
--- a/web/webqtl/textUI/cmdCorrelation.py
+++ /dev/null
@@ -1,325 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-import os
-import string
-from math import *
-import time
-
-import reaper
-
-from base import webqtlConfig
-from utility import webqtlUtil
-from cmdClass import cmdClass
-
-
-#########################################
-# Correlation Class
-#########################################
-class cmdCorrelation(cmdClass):
-
- calFunction = 'webqtlUtil.calCorrelation'
-
- def __init__(self,fd=None):
-
- cmdClass.__init__(self,fd)
-
- if not webqtlConfig.TEXTUI:
- self.contents.append("Please send your request to http://robot.genenetwork.org")
- return
-
-
- self.example = '###Example : <a href="%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&searchdb=BXDPublish&return=500&sort=pvalue">%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&searchdb=BXDPublish&return=500&sort=pvalue</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID)
-
- if self.accessError:
- return
-
- self.searchDB = self.data.getvalue('searchdb')
- if not self.searchDB or self.error:
- self.contents.append("###Error: source trait doesn't exist or no target database was given")
- self.contents.append(self.example)
- self.contents.append(self.accessCode)
- return
-
- try:
- self.returnNumber = int(self.data.getvalue('return'))
- except:
- self.returnNumber = None
-
- self.sort = self.data.getvalue('sort')
-
- prefix, dbId = self.getDBId(self.database)
- if not prefix or not dbId or (self.probe and string.lower(self.probe) in ("all","mm","pm")):
- self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.")
- self.contents.append(self.example)
- self.contents.append(self.accessCode)
- return
- RISet = self.getRISet(prefix, dbId)
- prefix2, dbId2 = self.getDBId(self.searchDB)
- if not prefix2 or not dbId2:
- self.contents.append("###Error: target database doesn't exist.")
- self.contents.append(self.example)
- self.contents.append(self.accessCode)
- return
- RISet2 = self.getRISet(prefix2, dbId2)
- if RISet2 != RISet:
- self.contents.append("###Error: target database has different Mouse InbredSet.")
- self.contents.append(self.example)
- self.contents.append(self.accessCode)
- return
-
- traitdata, heads = self.getTraitData(prefix, dbId, self.probeset, self.probe)
- if not traitdata:
- self.contents.append("###Error: source trait doesn't exist.")
- self.contents.append(self.example)
- self.contents.append(self.accessCode)
- return
-
- StrainNames = []
- sourceTrait = []
- StrainIds = []
-
- #XZ, Jan 27, 2011: Only the strains that are of the same inbredset are used to calculate correlation.
- for item in traitdata:
- one_strain_name = item[0]
- one_strain_value = item[1]
-
- self.cursor.execute('SELECT Strain.Id from Strain,StrainXRef, InbredSet WHERE Strain.Name="%s" and Strain.Id = StrainXRef.StrainId and StrainXRef.InbredSetId = InbredSet.Id and InbredSet.Name = "%s"' % (one_strain_name, RISet2))
- Results = self.cursor.fetchall()
- if Results:
- StrainIds.append('%d' % Results[0][0])
- StrainNames.append( one_strain_name )
- sourceTrait.append( one_strain_value )
-
- correlationArray = []
-
- useFastMethod = False
- if prefix2 == "ProbeSet":
- DatabaseFileName = self.getFileName( target_db_id=dbId2 )
- DirectoryList = os.listdir(webqtlConfig.TEXTDIR) ### List of existing text files. Used to check if a text file already exists
- if DatabaseFileName in DirectoryList:
- useFastMethod = True
-
- if useFastMethod:
- datasetFile = open(webqtlConfig.TEXTDIR+DatabaseFileName,'r')
-
- #XZ, 01/08/2009: read the first line
- line = datasetFile.readline()
- dataset_strains = webqtlUtil.readLineCSV(line)[1:]
-
- #XZ, 01/08/2009: This step is critical. It is necessary for this new method.
- _newvals = []
- for item in dataset_strains:
- if item in StrainNames:
- _newvals.append(sourceTrait[StrainNames.index(item)])
- else:
- _newvals.append('None')
-
- nnCorr = len(_newvals)
-
-
- for line in datasetFile:
- traitdata=webqtlUtil.readLineCSV(line)
- traitdataName = traitdata[0]
- traitvals = traitdata[1:]
-
- corr,nOverlap = webqtlUtil.calCorrelationText(traitvals,_newvals,nnCorr)
- traitinfo = [traitdataName,corr,nOverlap]
- correlationArray.append( traitinfo )
-
- #calculate correlation with slow method
- else:
- correlationArray = self.calCorrelation(sourceTrait, self.readDB(StrainIds, prefix2, dbId2) )
-
- correlationArray.sort(self.cmpCorr) #XZ: Do not forget the sort step
-
- if not self.returnNumber:
- correlationArray = correlationArray[:100]
- else:
- if self.returnNumber < len(correlationArray):
- correlationArray = correlationArray[:self.returnNumber]
- NN = len(correlationArray)
- for i in range(NN):
- nOverlap = correlationArray[i][-1]
- corr = correlationArray[i][-2]
- if nOverlap < 3:
- corrPValue = 1.0
- else:
- if abs(corr) >= 1.0:
- corrPValue = 0.0
- else:
- ZValue = 0.5*log((1.0+corr)/(1.0-corr))
- ZValue = ZValue*sqrt(nOverlap-3)
- corrPValue = 2.0*(1.0 - reaper.normp(abs(ZValue)))
- correlationArray[i].append(corrPValue)
- if self.sort == 'pvalue':
- correlationArray.sort(self.cmpPValue)
-
- if prefix2 == 'Publish':
- self.contents.append("RecordID\tCorrelation\t#Strains\tp-value")
- elif prefix2 == 'Geno':
- self.contents.append("Locus\tCorrelation\t#Strains\tp-value")
- else:
- pass
-
- if prefix2 == 'Publish' or prefix2 == 'Geno':
- for item in correlationArray:
- self.contents.append("%s\t%2.6f\t%d\t%2.6f" % tuple(item))
- else:
- id = self.data.getvalue('id')
- if id == 'yes':
- self.contents.append("ProbesetID\tCorrelation\t#Strains\tp-value\tGeneID")
- for item in correlationArray:
- query = """SELECT GeneID from %s WHERE Name = '%s'""" % (prefix2,item[0])
- self.cursor.execute(query)
- results = self.cursor.fetchall()
- if not results:
- item = item + [None]
- else:
- item = item + list(results[0])
- self.contents.append("%s\t%2.6f\t%d\t%2.6f\t%s" % tuple(item))
- elif id == 'only':
- self.contents.append("GenID")
- for item in correlationArray:
- query = """SELECT GeneID from %s WHERE Name = '%s'""" % (prefix2,item[0])
- self.cursor.execute(query)
- results = self.cursor.fetchall()
- if not results:
- self.contents.append('None')
- else:
- self.contents.append(results[0][0])
- else:
- self.contents.append("ProbesetID\tCorrelation\t#Strains\tp-value")
- for item in correlationArray:
- self.contents.append("%s\t%2.6f\t%d\t%2.6f" % tuple(item))
-
-
-
-
- def getFileName(self, target_db_id):
-
- query = 'SELECT Id, FullName FROM ProbeSetFreeze WHERE Id = %s' % target_db_id
- self.cursor.execute(query)
- result = self.cursor.fetchone()
- Id = result[0]
- FullName = result[1]
- FullName = FullName.replace(' ','_')
- FullName = FullName.replace('/','_')
-
- FileName = 'ProbeSetFreezeId_' + str(Id) + '_FullName_' + FullName + '.txt'
-
- return FileName
-
-
-
- def calCorrelation(self,source,target):
- allcorrelations = []
- NN = len(source)
-
- if len(source) != len(target[0]) - 1:
- return allcorrelations
- else:
- for traitData in target:
- corr,nOverlap = eval("%s(traitData[1:],source,NN)" % self.calFunction)
- traitinfo = [traitData[0],corr,nOverlap]
- allcorrelations.append(traitinfo)
-
- return allcorrelations
-
- def cmpCorr(self,A,B):
- try:
- if abs(A[1]) < abs(B[1]):
- return 1
- elif abs(A[1]) == abs(B[1]):
- return 0
- else:
- return -1
- except:
- return 0
-
- def cmpPValue(self,A,B):
- try:
- if A[-1] > B[-1]:
- return 1
- elif A[-1] == B[-1]:
- return 0
- else:
- return -1
- except:
- return 0
-
-
- def readDB(self, StrainIds=[], prefix2='', dbId2=''):
-
- #retrieve data from target database
- nnn = len(StrainIds) / 25
- if len(StrainIds) % 25:
- nnn += 1
- oridata = []
- for step in range(nnn):
- temp = []
- StrainIdstep = StrainIds[step*25:min(len(StrainIds), (step+1)*25)]
- for item in StrainIdstep:
- temp.append('T%s.value' % item)
- #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=cor&probeset=100001_at&probe=136415&db=bra08-03MAS5&searchdb=BXDPublish&return=500&sort=pvalue
- if prefix2 == "Publish":
- query = "SELECT PublishXRef.Id, "
- dataStartPos = 1
- query += string.join(temp,', ')
- query += ' from (PublishXRef, PublishFreeze)\n'
- #XZ, 03/05/2009: Xiaodong changed Data to PublishData
- for item in StrainIdstep:
- query += 'left join PublishData as T%s on T%s.Id = PublishXRef.DataId and T%s.StrainId=%s\n' %(item,item,item,item)
- query += "WHERE PublishXRef.InbredSetId = PublishFreeze.InbredSetId and PublishFreeze.Id = %d" % (dbId2, )
- #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=cor&probeset=100001_at&probe=136415&db=bra08-03MAS5&searchdb=HC_M2_1005_M&return=500&sort=pvalue
- #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=cor&probeset=100001_at&probe=136415&db=bra08-03MAS5&searchdb=BXDGeno&return=500&sort=pvalue
- else:
- query = "SELECT %s.Name," % prefix2
- query += string.join(temp,', ')
- query += ' from (%s, %sXRef, %sFreeze) \n' % (prefix2,prefix2,prefix2)
- #XZ, 03/05/2009: Xiaodong changed Data to %sData
- for item in StrainIdstep:
- query += 'left join %sData as T%s on T%s.Id = %sXRef.DataId and T%s.StrainId=%s\n' %(prefix2,item,item,prefix2,item,item)
- query += "WHERE %sXRef.%sFreezeId = %sFreeze.Id and %sFreeze.Id = %d and %s.Id = %sXRef.%sId" % (prefix2, prefix2, prefix2, prefix2, dbId2, prefix2, prefix2, prefix2)
- self.cursor.execute(query)
- results = self.cursor.fetchall()
- if not results:
- self.contents.append("###Error: target database doesn't exist.")
- self.contents.append(self.example)
- self.contents.append(self.accessCode)
- return
- oridata.append(results)
-
- datasize = len(oridata[0])
- targetTrait = []
- for j in range(datasize):
- traitdata = list(oridata[0][j])
- for i in range(1,nnn):
- traitdata += list(oridata[i][j][1:])
- targetTrait.append(traitdata)
-
- return targetTrait
-
diff --git a/web/webqtl/textUI/cmdGeno.py b/web/webqtl/textUI/cmdGeno.py
deleted file mode 100755
index 8dd0f924..00000000
--- a/web/webqtl/textUI/cmdGeno.py
+++ /dev/null
@@ -1,118 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-import string
-import os
-
-import reaper
-
-from base import webqtlConfig
-from cmdClass import cmdClass
-
-#########################################
-# Geno Class
-#########################################
-class cmdGeno(cmdClass):
-
- def __init__(self,fd=None):
-
- cmdClass.__init__(self,fd)
-
- if not webqtlConfig.TEXTUI:
- self.contents.append("Please send your request to http://robot.genenetwork.org")
- return
-
- if self.accessError:
- return
- self.error = 0
- self.RISet = None
- self.chr = None
- self.dataset = None
- self.strainList = []
- try:
- self.RISet = self.data.getvalue('riset')
- if not self.RISet:
- raise ValueError
- except:
- self.error = 1
- self.contents.append('###Example : http://www.genenetwork.org%s%s?cmd=%s&riset=BXD&chr=1' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID))
- return
- try:
- self.format = self.data.getvalue('format')[:3]
- except:
- self.format = 'row'
-
- try:
- self.dataset = reaper.Dataset()
- try:
- self.dataset.read(os.path.join(webqtlConfig.GENODIR, self.RISet + '.geno'))
- except:
- self.dataset.read(os.path.join(webqtlConfig.GENODIR, self.RISet.upper() + '.geno'))
- self.strainList = list(self.dataset.prgy)
- except:
- self.error = 1
- #traceback.print_exc()
- self.contents.append('###The name of RISet is incorrect')
- return
-
- try:
- self.chr = self.data.getvalue('chr')
- if self.chr:
- if self.chr == 'X' or self.chr == 'x':
- self.chr = '20'
- self.chr = int(self.chr)
- except:
- pass
-
- self.readGeno()
-
- def readGeno(self):
- try:
- table = [['Chr'] + ['Locus'] + self.strainList]
- if self.chr:
- chr = self.dataset[self.chr-1]
- for locus in chr:
- items = string.split(string.join(locus.genotext, " "))
- items = [chr.name] + [locus.name] + items
- table += [items]
- else:
- for chr in self.dataset:
- for locus in chr:
- items = string.split(string.join(locus.genotext, " "))
- items = [chr.name] + [locus.name] + items
- table += [items]
- if self.format == 'col':
- table = [[r[col] for r in table] for col in range(1, len(table[0]))]
- table[0][0] = 'Line'
- lines = string.join(map(lambda x: string.join(x, '\t'), table), '\n')
- self.contents.append(lines)
- except:
- self.contents =['###Error: Read file error or name of chromosome is incorrect']
- #traceback.print_exc()
- return
-
-
-
diff --git a/web/webqtl/textUI/cmdGet.py b/web/webqtl/textUI/cmdGet.py
deleted file mode 100755
index a11c97a3..00000000
--- a/web/webqtl/textUI/cmdGet.py
+++ /dev/null
@@ -1,86 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-import string
-
-from base import webqtlConfig
-from cmdClass import cmdClass
-
-#########################################
-# Get trait value Class
-#########################################
-class cmdGet(cmdClass):
- def __init__(self,fd=None):
-
- cmdClass.__init__(self,fd)
-
- if not webqtlConfig.TEXTUI:
- self.contents.append("Please send your request to http://robot.genenetwork.org")
- return
-
- self.example = '###Example : <a href="%s%s?cmd=%s&probeset=100001_at&db=bra03-03Mas5&probe=all">%s%s?cmd=%s&probeset=100001_at&db=bra03-03Mas5&probe=all</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID)
- if self.accessError:
- return
- if not self.error:
- self.readDB()
- else:
- self.contents.append(self.example)
- self.contents.append(self.accessCode)
-
- def readDB(self):
- prefix, dbId = self.getDBId(self.database)
-
- traitdata, heads = self.getTraitData(prefix, dbId, self.probeset, self.probe)
- try:
- if not traitdata:
- raise ValueError
- traitdata = heads + list(traitdata)
- if self.format == 'col':
- self.formatCols(traitdata)
- else:
- self.formatRows(traitdata)
- except:
- self.contents.append('Error: no record was found')
- self.contents.append(self.accessCode)
- return
-
- def formatCols(self, traitdata):
- for item in traitdata:
- lines = []
- for item2 in item:
- lines.append(item2)
- lines = string.join(map(str,lines), '\t')
- self.contents.append(lines)
-
- def formatRows(self, traitdata):
- for i in range(len(traitdata[0])):
- lines = []
- for j in range(len(traitdata)):
- lines.append(traitdata[j][i])
- lines = string.join(map(str,lines), '\t')
- self.contents.append(lines)
-
-
diff --git a/web/webqtl/textUI/cmdHelp.py b/web/webqtl/textUI/cmdHelp.py
deleted file mode 100755
index 754ff5b5..00000000
--- a/web/webqtl/textUI/cmdHelp.py
+++ /dev/null
@@ -1,105 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-import string
-
-from base import webqtlConfig
-from base.admin import ADMIN_tissue_alias
-from cmdClass import cmdClass
-
-#########################################
-# Help Class
-#########################################
-
-#XZ, 03/23/2009: There are several issues need attention.
-#1. Some probeset datasets are not added into DBList.
-#2. Do NOT show confidential datasets.
-#3. Get rid of ADMIN_tissue_alias. We should use info from database instead.
-
-class cmdHelp(cmdClass):
- def __init__(self,fd=None):
-
- cmdClass.__init__(self,fd)
-
- if not webqtlConfig.TEXTUI:
- self.contents.append("Please send your request to http://robot.genenetwork.org")
- return
-
-
- machineParse = self.data.getvalue('parse')
- topic = self.data.getvalue('topic')
- if topic:
- topic = topic.lower()
- if topic == 'tissue':
- self.contents.append("%s%s| %s" %("Tissue", ' '*(50-len("Tissue")), "Tissue Abbreviations"))
- self.contents.append("%s%s| %s" %("", ' '*50, "(Separated by space, case insensitive)"))
- self.contents.append("%s|%s" %('_'*50, '_'*40))
-
- keys = ADMIN_tissue_alias.keys()
- keys.sort()
- for key in keys:
- self.contents.append("%s%s| %s" % (key , ' '*(50-len(key)), string.join(ADMIN_tissue_alias[key], " ")))
- self.contents.append("%s|%s" %('_'*50, '_'*40))
- else:
- pass
- else:
- self.contents = ["#Use database code table below to access data", "#For machine parse friendly output please use",
- "#http://www.genenetwork.org%s%s?cmd=help&parse=machine" % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)]
- self.cursor.execute("""(SELECT DBType.Name, DBList.FreezeId, DBList.Code, ProbeSetFreeze.CreateTime as Time
- from ProbeSetFreeze, DBType, DBList WHERE DBType.Id = DBList.DBTypeId and
- DBType.Name = 'ProbeSet' and DBList.FreezeId = ProbeSetFreeze.Id and
- ProbeSetFreeze.public > %d order by ProbeSetFreeze.CreateTime ,DBList.Name, DBList.Id)
- UNION
- (SELECT DBType.Name, DBList.FreezeId, DBList.Code, PublishFreeze.CreateTime as Time
- from PublishFreeze, DBType, DBList WHERE DBType.Id = DBList.DBTypeId and
- DBType.Name = 'Publish' and DBList.FreezeId = PublishFreeze.Id order by
- PublishFreeze.CreateTime ,DBList.Name, DBList.Id)
- UNION
- (SELECT DBType.Name, DBList.FreezeId, DBList.Code, GenoFreeze.CreateTime
- from GenoFreeze, DBType, DBList WHERE DBType.Id = DBList.DBTypeId and
- DBType.Name = 'Geno' and DBList.FreezeId = GenoFreeze.Id order by
- GenoFreeze.CreateTime ,DBList.Name, DBList.Id)""" % webqtlConfig.PUBLICTHRESH)
- dbs = self.cursor.fetchall()
- if machineParse =="machine":
- pass
- else:
- self.contents.append("\n")
- self.contents.append("%s%s| %s" %("Database_Name", ' '*(50-len("Database_Name")), "Database_Access_Code_Name"))
- self.contents.append("%s|%s" %('_'*50, '_'*40))
- for dbInfo in dbs:
- self.cursor.execute('SELECT FullName from %sFreeze WHERE Id = %d and public > %d' % (dbInfo[0], dbInfo[1],webqtlConfig.PUBLICTHRESH))
- results = self.cursor.fetchall()
- if not results:
- pass
- else:
- if machineParse =="machine":
- self.contents.append(results[0][0]+ ',' +dbInfo[2])
- else:
- self.contents.append("%s%s| %s" %(results[0][0], ' '*(50-len(results[0][0])), dbInfo[2]))
- self.contents.append("%s|%s" %('_'*50, '_'*40))
-
-
-
diff --git a/web/webqtl/textUI/cmdInterval.py b/web/webqtl/textUI/cmdInterval.py
deleted file mode 100755
index 0b97c7c3..00000000
--- a/web/webqtl/textUI/cmdInterval.py
+++ /dev/null
@@ -1,174 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-import string
-import os
-
-import reaper
-
-from base import webqtlConfig
-from cmdClass import cmdClass
-
-#########################################
-# Interval Mapping Class
-#########################################
-class cmdInterval(cmdClass):
-
- def __init__(self,fd=None):
-
- cmdClass.__init__(self,fd)
-
- if not webqtlConfig.TEXTUI:
- self.contents.append("Please send your request to http://robot.genenetwork.org")
- return
-
-
- self.example = '###Example : <a href="%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=pos&return=100&chr=12">%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=pos&return=100&chr=12</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID)
- if self.accessError:
- return
- self.sort = None
- self.step = 0.01
- self.peak = 1
- self.chr = None
- self.sort = None
- self.returnnumber = 20
- if self.error:
- self.error = 1
- self.contents.append(self.example)
- return
- else:
- try:
- self.sort = self.data.getvalue('sort')
- if string.lower(self.sort) == 'pos':
- self.sort = 'pos'
- else:
- self.sort = 'lrs'
- except:
- self.sort = None
-
- try:
- self.returnnumber = int(self.data.getvalue('return'))
- except:
- self.returnnumber = 20
- try:
- self.chr = self.data.getvalue('chr')
- except:
- self.chr = None
-
- self.readDB()
-
- def readDB(self):
- prefix, dbId = self.getDBId(self.database)
- if not prefix or not dbId or (self.probe and string.lower(self.probe) in ("all","mm","pm")):
- self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.")
- self.contents.append(self.example)
- self.contents.append(self.accessCode)
- return
- RISet = self.getRISet(prefix, dbId)
- traitdata, heads = self.getTraitData(prefix, dbId, self.probeset, self.probe)
- if not traitdata:
- self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.")
- self.contents.append(self.example)
- self.contents.append(self.accessCode)
- return
-
- dataset0 = reaper.Dataset()
- dataset0.read(os.path.join(webqtlConfig.GENODIR, RISet + '.geno'))
- strainList = list(dataset0.prgy)
- dataset = dataset0.addinterval()
- if self.chr != None:
- for _chr in dataset:
- if string.lower(_chr.name) == string.lower(self.chr):
- dataset.chromosome = [_chr]
- break
-
- strains = []
- trait = []
- _prgy = dataset.prgy
- for item in traitdata:
- if item[0] in _prgy:
- strains.append(item[0])
- trait.append(item[1])
-
- qtlscan = dataset.regression(strains, trait)
- LRS = dataset.permutation(strains, trait)
- nperm = len(LRS)
-
- #print inter1[0]
- returnPeak = []
- nqtl = len(qtlscan)
- if self.peak:
- for i in range(nqtl):
- if i == 0 or qtlscan[i].locus.chr != qtlscan[i-1].locus.chr:
- if qtlscan[i].lrs < qtlscan[i+1].lrs:
- continue
- elif i == nqtl-1 or qtlscan[i].locus.chr != qtlscan[i+1].locus.chr:
- if qtlscan[i].lrs < qtlscan[i-1].lrs:
- continue
- else:
- if qtlscan[i].lrs < qtlscan[i+1].lrs or qtlscan[i].lrs < qtlscan[i-1].lrs:
- continue
- returnPeak.append(qtlscan[i])
- else:
- returnPeak = qtlscan[:]
-
- if returnPeak:
- self.contents.append("Locus\tLRS\tChr\tAdditive\tp-value\tcM")
- qtlresult = []
- for item in returnPeak:
- p_value = reaper.pvalue(item.lrs,LRS)
- qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value, item.locus.cM))
- if self.sort == 'lrs':
- qtlresult.sort(self.cmpLRS2)
- for item in qtlresult:
- self.contents.append("%s\t%2.4f\t%s\t%2.4f\t%1.4f\t%s" % item)
- else:
- self.contents.append("###Error: Error occurs while regression.")
- return
-
- def cmpPValue(self,A,B):
- try:
- if A[-1] > B[-1]:
- return 1
- elif A[-1] == B[-1]:
- return 0
- else:
- return -1
- except:
- return 0
-
- def cmpLRS2(self,A,B):
- try:
- if A[1] < B[1]:
- return 1
- elif A[1] == B[1]:
- return 0
- else:
- return -1
- except:
- return 0
-
-
diff --git a/web/webqtl/textUI/cmdMap.py b/web/webqtl/textUI/cmdMap.py
deleted file mode 100755
index 1fbff5a5..00000000
--- a/web/webqtl/textUI/cmdMap.py
+++ /dev/null
@@ -1,144 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-import string
-import os
-
-import reaper
-
-from base import webqtlConfig
-from cmdClass import cmdClass
-
-
-#########################################
-# Mapping Class
-#########################################
-class cmdMap(cmdClass):
-
- def __init__(self,fd=None):
-
- cmdClass.__init__(self,fd)
-
- if not webqtlConfig.TEXTUI:
- self.contents.append("Please send your request to http://robot.genenetwork.org")
- return
-
- self.example = '###Example : <a href="%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=lrs&return=20">%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=lrs&return=20</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID)
- if self.accessError:
- return
- try:
- self.returnnumber = int(self.data.getvalue('return'))
- except:
- self.returnnumber = None
-
- if self.error:
- self.contents.append(self.example)
- self.contents.append(self.accessCode)
- else:
- self.sort = self.data.getvalue('sort')
- self.readDB()
-
- def readDB(self):
- prefix, dbId = self.getDBId(self.database)
- if not prefix or not dbId or (self.probe and string.lower(self.probe) in ("all","mm","pm")):
- self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.")
- self.contents.append(self.example)
- self.contents.append(self.accessCode)
- return
- RISet = self.getRISet(prefix, dbId)
- traitdata, heads = self.getTraitData(prefix, dbId, self.probeset, self.probe)
- if not traitdata:
- self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.")
- self.contents.append(self.example)
- self.contents.append(self.accessCode)
- return
-
- dataset = reaper.Dataset()
- dataset.read(os.path.join(webqtlConfig.GENODIR, RISet + '.geno'))
- strainList = list(dataset.prgy)
-
- strains = []
- trait = []
- _prgy = dataset.prgy
- for item in traitdata:
- if item[0] in _prgy:
- strains.append(item[0])
- trait.append(item[1])
-
- qtlscan = dataset.regression(strains, trait)
- LRS = dataset.permutation(strains, trait)
- nperm = len(LRS)
- if qtlscan:
- self.contents.append("Locus\tLRS\tChr\tAdditive\tp-value")
- qtlresult = []
- if self.returnnumber:
- self.returnnumber = min(self.returnnumber,len(qtlscan))
- if self.sort == 'lrs':
- qtlscan.sort(self.cmpLRS)
- for item in qtlscan[:self.returnnumber]:
- p_value = reaper.pvalue(item.lrs,LRS)
- qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value))
- else:#sort by position
- qtlscan2 = qtlscan[:]
- qtlscan2.sort(self.cmpLRS)
- LRSthresh = qtlscan2[self.returnnumber].lrs
- for item in qtlscan:
- if item.lrs >= LRSthresh:
- p_value = reaper.pvalue(item.lrs,LRS)
- qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value))
- else:
- for item in qtlscan:
- p_value = reaper.pvalue(item.lrs,LRS)
- qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value))
- if self.sort == 'lrs':
- qtlresult.sort(self.cmpLRS2)
- for item in qtlresult:
- self.contents.append("%s\t%2.5f\t%s\t%2.5f\t%1.5f" % item)
- else:
- self.contents.append("###Error: Error occurs while regression.")
- return
-
- def cmpLRS(self,A,B):
- try:
- if A.lrs < B.lrs:
- return 1
- elif A.lrs == B.lrs:
- return 0
- else:
- return -1
- except:
- return 0
-
- def cmpLRS2(self,A,B):
- try:
- if A[1] < B[1]:
- return 1
- elif A[1] == B[1]:
- return 0
- else:
- return -1
- except:
- return 0
diff --git a/web/webqtl/textUI/cmdSearchGene.py b/web/webqtl/textUI/cmdSearchGene.py
deleted file mode 100755
index c2c71815..00000000
--- a/web/webqtl/textUI/cmdSearchGene.py
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-import string
-
-from cmdClass import cmdClass
-from search.TextSearchPage import TextSearchPage
-
-#########################################
-# Search Gene Symbol PAGE
-#########################################
-class cmdSearchGene(cmdClass):
- def __init__(self,fd):
- #example
- cmdClass.__init__(self,fd)
- self.page = None
- self.text = ""
- fd.geneName = fd.formdata.getvalue('gene')
- fd.returnFmt = fd.formdata.getvalue('format', 'html')
- if fd.geneName:
- fd.geneName = string.strip(fd.geneName)
- fd.refseq = fd.formdata.getvalue('refseq')
- if fd.refseq:
- fd.refseq = string.strip(fd.refseq)
- fd.genbankid = fd.formdata.getvalue('genbankid')
- if fd.genbankid:
- fd.genbankid = string.strip(fd.genbankid)
- fd.geneid = fd.formdata.getvalue('geneid')
- if fd.geneid:
- fd.geneid = string.strip(fd.geneid)
- if 1:
- if not (fd.geneName or fd.refseq or fd.genbankid or fd.geneid):
- raise "ValueError"
- fd.searchAlias = fd.formdata.getvalue('alias')
- if fd.searchAlias != '1':
- fd.searchAlias = None
- self.page = TextSearchPage(fd)
- if fd.returnFmt != 'text':
- pass
- else:
- self.text = self.page.output
- self.page = None
- elif "ValueError":
- self.text = "You need to submit a Gene name, a Refseq ID, or a GenBank ID"
- else:
- self.text = "Error occurs while searching the database"
-
diff --git a/web/webqtl/textUI/cmdShowEditing.py b/web/webqtl/textUI/cmdShowEditing.py
deleted file mode 100755
index 918e83a7..00000000
--- a/web/webqtl/textUI/cmdShowEditing.py
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-from cmdClass import cmdClass
-from showTrait.ShowTraitPage import ShowTraitPage
-
-
-#########################################
-# SHOW DATA-EDITING PAGE
-#########################################
-class cmdShowEditing(cmdClass):
- def __init__(self,fd):
- ###example = http://www.webqtl.org/cgi-bin/beta/WebQTL?cmd=snp&chr=1&start=0&end=21345677
- cmdClass.__init__(self,fd)
- self.page = None
- prefix, dbId = self.getDBId(self.database)
- try:
- if not prefix or not dbId:
- raise ValueError
- self.cursor.execute('SELECT Name from %sFreeze WHERE Id=%d' % (prefix, dbId))
- database = self.cursor.fetchall()[0][0]
- traitInfos = (database,self.probeset,self.probe)
- self.page = ShowTraitPage(fd,traitInfos)
- #self = page
- except:
- print "Database Name Incorrect"
-
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-20 01:28:19 +0000