Refactored dir name dbFunction to db

2 files changed, 0 insertions, 267 deletions

diff --git a/wqflask/dbFunction/__init__.py b/wqflask/dbFunction/__init__.py
deleted file mode 100644
index e69de29b..00000000
--- a/wqflask/dbFunction/__init__.py
+++ /dev/null
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