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

1 files changed, 0 insertions, 265 deletions

diff --git a/web/webqtl/dbFunction/webqtlDatabaseFunction.py b/web/webqtl/dbFunction/webqtlDatabaseFunction.py
deleted file mode 100755
index 772e0526..00000000
--- a/web/webqtl/dbFunction/webqtlDatabaseFunction.py
+++ /dev/null
@@ -1,265 +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 Xiaodong Zhou 2011/Jan/20
-
-#webqtlDatabaseFunction.py
-#
-#This file consists of various database related functions; the names are generally self-explanatory. 
-
-import MySQLdb
-import string
-from base import webqtlConfig
-
-###########################################################################
-#output: cursor instance
-#function: connect to database and return cursor instance
-###########################################################################
-def getCursor():
-    try:
-        con = MySQLdb.Connect(db=webqtlConfig.DB_NAME, host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER, passwd=webqtlConfig.DB_PASSWD)
-        cursor = con.cursor()
-        return cursor
-    except:
-        return None
-
-
-
-###########################################################################
-#input: cursor, groupName (string)
-#output: mappingMethodId (int) info, value will be Null or else
-#function: retrieve mappingMethodId info from InbredSet table  
-###########################################################################	
-
-def getMappingMethod(cursor=None, groupName=None):
-	cursor.execute("select MappingMethodId from InbredSet where Name= '%s'" % groupName)
-	mappingMethodId = cursor.fetchone()[0]
-	return mappingMethodId
-
-###########################################################################
-#input: cursor, inbredSetId (int), strainId (int)
-#output: isMappingId (bull) info, value will be 0,1,2 or else, 0 or Null means 
-# "can not do mapping", >0 means "can do mapping", >1 means "there exsists 
-# redundant data, user needs to choose one to do mapping function"
-#function: retrieve isMappingId info from StrainXRef table  
-###########################################################################	
-	
-def isMapping(cursor=None, inbredSetId=None, strainId=None): 
-	cursor.execute("select IsMapping from StrainXRef where InbredSetId='%d' and StrainId = '%d'" %(inbredSetId, strainId))
-	isMappingId = cursor.fetchone()[0]
-	return isMappingId
-
-###########################################################################
-#input: cursor, groupName (string)
-#output: all species data info (array), value will be Null or else
-#function: retrieve all species info from Species table  
-###########################################################################	
-
-def getAllSpecies(cursor=None):
-	cursor.execute("select Id, Name, MenuName, FullName, TaxonomyId,OrderId from Species Order by OrderId")
-	allSpecies = cursor.fetchall()
-	return allSpecies
-
-###########################################################################
-#input: cursor, RISet (string)
-#output: specie's name (string), value will be None or else
-#function: retrieve specie's name info based on RISet  
-###########################################################################	
-
-def retrieveSpecies(cursor=None, RISet=None):
-	try:
-		cursor.execute("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % RISet)
-		return cursor.fetchone()[0]
-	except:
-		return None
-
-###########################################################################
-#input: cursor, RISet (string)
-#output: specie's Id (string), value will be None or else
-#function: retrieve specie's Id info based on RISet  
-###########################################################################	
-		
-def retrieveSpeciesId(cursor=None, RISet=None):
-	try:
-		cursor.execute("select SpeciesId from InbredSet where Name = '%s'" % RISet)
-		return cursor.fetchone()[0]
-	except:
-		return None
-
-###########################################################################
-# input: cursor
-# output: tissProbeSetFreezeIdList (list),
-#         nameList (list),
-#         fullNameList (list)
-# function: retrieve all TissueProbeSetFreezeId,Name,FullName info
-#           from TissueProbeSetFreeze table.
-#           These data will listed in the dropdown menu in the first page of Tissue Correlation
-###########################################################################
-
-def getTissueDataSet(cursor=None):
-	tissProbeSetFreezeIdList=[]
-	nameList =[]
-	fullNameList = []
-	
-	query = "select Id,Name,FullName from TissueProbeSetFreeze; "
-	try:
-		cursor.execute(query)
-		result = cursor.fetchall()
-	
-		for row in result:
-			tissProbeSetFreezeIdList.append(row[0])
-			nameList.append(row[1])
-			fullNameList.append(row[2])
-	except:
-		return None	
-		
-	return tissProbeSetFreezeIdList,nameList,fullNameList	
-	
-###########################################################################
-# input: cursor,GeneSymbol (string), and TissueProbeSetFreezeId (string)
-# output: geneId (string), dataId (string)
-# function: retrieve geneId and DataId from TissueProbeSetXRef table
-###########################################################################
-
-def getGeneIdDataIdForTissueBySymbol(cursor=None, GeneSymbol=None, TissueProbeSetFreezeId= 0):
-	query ="select GeneId, DataId from TissueProbeSetXRef where Symbol = '%s' and TissueProbeSetFreezeId=%s order by Mean desc" %(GeneSymbol,TissueProbeSetFreezeId)
-	try:
-		cursor.execute(query)
-		result = cursor.fetchone()
-		geneId = result[0]
-		dataId = result[1]
-	except:
-		geneId = 0
-		dataId = 0
-		
-	return geneId,dataId
-
-###########################################################################
-# input: cursor, TissueProbeSetFreezeId (int)
-# output: chipId (int)
-# function: retrieve chipId from TissueProbeFreeze table 
-###########################################################################
-
-def getChipIdByTissueProbeSetFreezeId(cursor=None, TissueProbeSetFreezeId=None):
-	query = "select TissueProbeFreezeId from TissueProbeSetFreeze where Id =%s" % TissueProbeSetFreezeId
-	try:
-		cursor.execute(query)
-		result = cursor.fetchone()
-		TissueProbeFreezeId = result[0]
-	except:
-		TissueProbeFreezeId =0
-		
-	query1 = "select ChipId from TissueProbeFreeze where Id =%s" % TissueProbeFreezeId
-	try:
-		cursor.execute(query1)
-		result1 = cursor.fetchone()
-		chipId = result1[0]
-	except:
-		chipId =0
-		
-	return chipId
-
-###########################################################################
-# input: cursor, TissueProbeSetFreezeId (int)
-# output: TissueCount (int)
-# function: retrieve how many tissue used in the specific dataset based on TissueProbeSetFreezeId
-###########################################################################
-def getTissueCountByTissueProbeSetFreezeId(cursor=None, TissueProbeSetFreezeId=None):
-	query1 ="select DataId from TissueProbeSetXRef where TissueProbeSetFreezeId =%s limit 1" % TissueProbeSetFreezeId
-	try:
-		cursor.execute(query1)
-		result1 = cursor.fetchone()
-		DataId = result1[0]
-		
-		query2 =" select count(*) from TissueProbeSetData where Id=%s" % DataId
-		try:
-			cursor.execute(query2)
-			result2 = cursor.fetchone()
-			TissueCount = result2[0]
-		except:
-			TissueCount =0
-	except:
-		TissueCount =0
-		
-	return TissueCount
-	
-###########################################################################
-# input: cursor, TissueProbeSetFreezeId (int)
-# output: DatasetName(string),DatasetFullName(string)
-# function: retrieve DatasetName, DatasetFullName based on TissueProbeSetFreezeId
-###########################################################################
-def getDatasetNamesByTissueProbeSetFreezeId(cursor=None, TissueProbeSetFreezeId=None):
-	query ="select Name, FullName from TissueProbeSetFreeze where Id=%s" % TissueProbeSetFreezeId
-	try:
-		cursor.execute(query)
-		result = cursor.fetchone()
-		DatasetName = result[0]
-		DatasetFullName =result[1]
-	except:
-		DatasetName =None
-		DatasetFullName =None
-				
-	return DatasetName, DatasetFullName
-	
-###########################################################################
-# input: cursor, geneIdLst (list)
-# output: geneIdSymbolPair(dict),key is geneId, value is geneSymbol
-# function: retrieve GeneId, GeneSymbol based on geneId List
-###########################################################################	
-def getGeneIdSymbolPairByGeneId(cursor=None, geneIdLst =None):
-	geneIdSymbolPair={}
-	for geneId in geneIdLst:
-		geneIdSymbolPair[geneId]=None
-
-	query ="select GeneId,GeneSymbol from GeneList where GeneId in (%s)" % string.join(geneIdLst, ", ")
-	try:
-		cursor.execute(query)
-		results = cursor.fetchall()
-		for item in results:
-			geneId =item[0]
-			geneSymbol =item[1]
-			geneIdSymbolPair[geneId]=geneSymbol
-	except:
-		geneIdSymbolPair=None
-				
-	return geneIdSymbolPair
-	
-	
-def updateTissueProbesetXRefByProbesetId(cursor=None, probesetId=None):
-	query ="select Symbol,GeneId,Chr,Mb,description, Probe_Target_Description from ProbeSet where Id =%s"%probesetId
-	try:
-		cursor.execute(query)
-		result =cursor.fetchone()
-	
-		updateQuery ='''
-				Update TissueProbeSetXRef 
-				Set Symbol='%s',GeneId='%s', Chr='%s', Mb='%s', description ='%s',Probe_Target_Description='%s'
-				where ProbesetId=%s
-				'''%(result[0],result[1],result[2],result[3],result[4],result[5],probesetId)
-				
-		cursor.execute(updateQuery)
-	
-	except:
-		return None
-		
\ No newline at end of file