1 files changed, 0 insertions, 180 deletions
diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py
index 2bc4745b..567e7375 100644
--- a/wqflask/db/webqtlDatabaseFunction.py
+++ b/wqflask/db/webqtlDatabaseFunction.py
@@ -57,185 +57,5 @@ def retrieve_species(group):
     return result
 
 
-def getMappingMethod(cursor=None, groupName=None):
-    return fetch1("select MappingMethodId from InbredSet where Name= '%s'" % groupName, "/cross/"+group+".json", lambda r: r["mapping_method_id"])[0]
-
-###########################################################################
-#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