From 93c1742a91c478667b8645c458cce2108eb24b14 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 23 Jun 2016 05:20:34 +0000
Subject: Refactored dir name dbFunction to db
---
wqflask/db/__init__.py | 0
wqflask/db/webqtlDatabaseFunction.py | 267 +++++++++++++++++++++++++++++++++++
2 files changed, 267 insertions(+)
create mode 100644 wqflask/db/__init__.py
create mode 100644 wqflask/db/webqtlDatabaseFunction.py
(limited to 'wqflask/db')
diff --git a/wqflask/db/__init__.py b/wqflask/db/__init__.py
new file mode 100644
index 00000000..e69de29b
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
--
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