Ran reindent.py recursively on wqflask directory

1 files changed, 146 insertions, 147 deletions

diff --git a/wqflask/dbFunction/webqtlDatabaseFunction.py b/wqflask/dbFunction/webqtlDatabaseFunction.py
index 772e0526..7e33da3f 100755
--- a/wqflask/dbFunction/webqtlDatabaseFunction.py
+++ b/wqflask/dbFunction/webqtlDatabaseFunction.py
@@ -26,7 +26,7 @@
 
 #webqtlDatabaseFunction.py
 #
-#This file consists of various database related functions; the names are generally self-explanatory. 
+#This file consists of various database related functions; the names are generally self-explanatory.
 
 import MySQLdb
 import string
@@ -49,63 +49,63 @@ def getCursor():
 ###########################################################################
 #input: cursor, groupName (string)
 #output: mappingMethodId (int) info, value will be Null or else
-#function: retrieve mappingMethodId info from InbredSet table  
-###########################################################################	
+#function: retrieve mappingMethodId info from InbredSet table
+###########################################################################
 
 def getMappingMethod(cursor=None, groupName=None):
-	cursor.execute("select MappingMethodId from InbredSet where Name= '%s'" % groupName)
-	mappingMethodId = cursor.fetchone()[0]
-	return mappingMethodId
+    cursor.execute("select MappingMethodId from InbredSet where Name= '%s'" % groupName)
+    mappingMethodId = cursor.fetchone()[0]
+    return mappingMethodId
 
 ###########################################################################
 #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 
+#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
+#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  
-###########################################################################	
+#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
+    cursor.execute("select Id, Name, MenuName, FullName, TaxonomyId,OrderId from Species Order by OrderId")
+    allSpecies = cursor.fetchall()
+    return allSpecies
 
 ###########################################################################
 #input: cursor, RISet (string)
 #output: specie's name (string), value will be None or else
-#function: retrieve specie's name info based on RISet  
-###########################################################################	
+#function: retrieve specie's name info based on RISet
+###########################################################################
 
 def retrieveSpecies(cursor=None, RISet=None):
-	try:
-		cursor.execute("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % RISet)
-		return cursor.fetchone()[0]
-	except:
-		return None
+    try:
+        cursor.execute("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % RISet)
+        return cursor.fetchone()[0]
+    except:
+        return None
 
 ###########################################################################
 #input: cursor, RISet (string)
 #output: specie's Id (string), value will be None or else
-#function: retrieve specie's Id info based on RISet  
-###########################################################################	
-		
+#function: retrieve specie's Id info based on RISet
+###########################################################################
+
 def retrieveSpeciesId(cursor=None, RISet=None):
-	try:
-		cursor.execute("select SpeciesId from InbredSet where Name = '%s'" % RISet)
-		return cursor.fetchone()[0]
-	except:
-		return None
+    try:
+        cursor.execute("select SpeciesId from InbredSet where Name = '%s'" % RISet)
+        return cursor.fetchone()[0]
+    except:
+        return None
 
 ###########################################################################
 # input: cursor
@@ -118,24 +118,24 @@ def retrieveSpeciesId(cursor=None, RISet=None):
 ###########################################################################
 
 def getTissueDataSet(cursor=None):
-	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	
-	
+    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)
@@ -143,42 +143,42 @@ def getTissueDataSet(cursor=None):
 ###########################################################################
 
 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
+    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 
+# 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
+    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)
@@ -186,80 +186,79 @@ def getChipIdByTissueProbeSetFreezeId(cursor=None, TissueProbeSetFreezeId=None):
 # 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
-	
+    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
-	
+    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
-	
-	
+    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
-		
\ No newline at end of file
+    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