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Diffstat (limited to 'wqflask/db/webqtlDatabaseFunction.py')
| -rw-r--r-- | wqflask/db/webqtlDatabaseFunction.py | 267 |
1 files changed, 267 insertions, 0 deletions
diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py new file mode 100644 index 00000000..e30929d2 --- /dev/null +++ b/wqflask/db/webqtlDatabaseFunction.py @@ -0,0 +1,267 @@ +# 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 |