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Diffstat (limited to 'wqflask/dbFunction/webqtlDatabaseFunction.py')
| -rw-r--r-- | wqflask/dbFunction/webqtlDatabaseFunction.py | 267 |
1 files changed, 0 insertions, 267 deletions
diff --git a/wqflask/dbFunction/webqtlDatabaseFunction.py b/wqflask/dbFunction/webqtlDatabaseFunction.py deleted file mode 100644 index e30929d2..00000000 --- a/wqflask/dbFunction/webqtlDatabaseFunction.py +++ /dev/null @@ -1,267 +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) - -from inspect import stack -from flask import Flask, g - -import MySQLdb -import string -import urllib2 -import json -from base import webqtlConfig -from utility.tools import USE_GN_SERVER, LOG_SQL -from utility.benchmark import Bench - -from utility.logger import getLogger -logger = getLogger(__name__ ) - -########################################################################### -#output: cursor instance -#function: connect to database and return cursor instance -########################################################################### -def getCursor(): - try: - logger.warning("Creating new MySQLdb cursor") - 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 - -def fetchone(query): - """Return tuple containing one row by calling SQL directly - - """ - with Bench("SQL",LOG_SQL): - def helper(query): - res = g.db.execute(query) - return res.fetchone() - callername = stack()[1][3] - return logger.sql(callername, query, helper) - -def gn_server(path): - """Return JSON record by calling GN_SERVER - - """ - with Bench("GN_SERVER",LOG_SQL): - res = urllib2.urlopen("http://localhost:8880/"+path) - rest = res.read() - res2 = json.loads(rest) - logger.info(res2) - return res2 - -def retrieve_species(group): - """Get the species of a group (e.g. returns string "mouse" on "BXD" - - """ - if USE_GN_SERVER: - result = gn_server("/cross/"+group+".json") - return result["species"] - else: - result = fetchone("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group)) - return result[0] - -def getMappingMethod(cursor=None, groupName=None): - if USE_GN_SERVER: - return gn_server("/cross/"+group+".json")["mapping_method_id"] - else: - return fetchone("select MappingMethodId from InbredSet where Name= '%s'" % groupName) - -########################################################################### -#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 - - -def retrieve_species_id(group): - return g.db.execute("select SpeciesId from InbredSet where Name = %s", (group)).fetchone()[0] - - -def getTissueDataSet(cursor=None): - """Retrieve all TissueProbeSetFreezeId,Name,FullName info from -TissueProbeSetFreeze table. These data will listed in the dropdown -menu in the first page of Tissue Correlation - - """ - 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 |