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-rwxr-xr-xwqflask/base/data_set.py22
-rwxr-xr-xwqflask/base/trait.py18
-rwxr-xr-xwqflask/utility/webqtlUtil.py17
-rwxr-xr-xwqflask/wqflask/docs.py4
-rwxr-xr-xwqflask/wqflask/show_trait/show_trait.py9
5 files changed, 25 insertions, 45 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index acfee3d4..d46e4363 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -392,6 +392,12 @@ class DatasetGroup(object):
Redis.set(key, json.dumps(self.samplelist))
Redis.expire(key, 60*5)
+ def all_samples_ordered(self):
+ result = []
+ lists = (self.parlist, self.f1list, self.samplelist)
+ [result.extend(l) for l in lists if l]
+ return result
+
def read_genotype_file(self):
'''Read genotype from .geno file instead of database'''
#if self.group == 'BXD300':
@@ -805,11 +811,11 @@ class PhenotypeDataSet(DataSet):
WHERE
PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = %s AND
- PublishFreeze.Id = %d AND PublishData.StrainId = Strain.Id
+ PublishFreeze.Id = %s AND PublishData.StrainId = Strain.Id
Order BY
Strain.Name
- """ % (trait, self.id)
- results = g.db.execute(query).fetchall()
+ """
+ results = g.db.execute(query, (trait, self.id)).fetchall()
return results
@@ -892,15 +898,17 @@ class GenotypeDataSet(DataSet):
left join GenoSE on
(GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId)
WHERE
- Geno.SpeciesId = %s AND Geno.Name = '%s' AND GenoXRef.GenoId = Geno.Id AND
+ Geno.SpeciesId = %s AND Geno.Name = %s AND GenoXRef.GenoId = Geno.Id AND
GenoXRef.GenoFreezeId = GenoFreeze.Id AND
- GenoFreeze.Name = '%s' AND
+ GenoFreeze.Name = %s AND
GenoXRef.DataId = GenoData.Id AND
GenoData.StrainId = Strain.Id
Order BY
Strain.Name
- """ % (webqtlDatabaseFunction.retrieve_species_id(self.group.name), trait, self.name)
- results = g.db.execute(query).fetchall()
+ """
+ results = g.db.execute(query,
+ (webqtlDatabaseFunction.retrieve_species_id(self.group.name),
+ trait, self.name)).fetchall()
return results
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 7f1170a9..4a088bc8 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -251,14 +251,7 @@ class GeneralTrait(object):
# Todo: is this necessary? If not remove
self.data.clear()
- if self.dataset.group.parlist:
- all_samples_ordered = (self.dataset.group.parlist +
- self.dataset.group.f1list +
- self.dataset.group.samplelist)
- elif self.dataset.group.f1list:
- all_samples_ordered = self.dataset.group.f1list + self.dataset.group.samplelist
- else:
- all_samples_ordered = self.dataset.group.samplelist
+ all_samples_ordered = self.dataset.group.all_samples_ordered()
if results:
for item in results:
@@ -299,6 +292,7 @@ class GeneralTrait(object):
""" % (self.name, self.dataset.id)
print("query is:", query)
+ assert self.name.isdigit()
trait_info = g.db.execute(query).fetchone()
#XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
@@ -337,10 +331,10 @@ class GeneralTrait(object):
trait_info = g.db.execute(query).fetchone()
#print("trait_info is: ", pf(trait_info))
else: #Temp type
- query = """SELECT %s FROM %s WHERE Name = %s
- """ % (string.join(self.dataset.display_fields,','),
- self.dataset.type, self.name)
- trait_info = g.db.execute(query).fetchone()
+ query = """SELECT %s FROM %s WHERE Name = %s"""
+ trait_info = g.db.execute(query,
+ (string.join(self.dataset.display_fields,','),
+ self.dataset.type, self.name)).fetchone()
if trait_info:
self.haveinfo = True
diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index 4d7981d9..f842dde0 100755
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -43,6 +43,7 @@ ParInfo ={
'BXH':['BHF1', 'HBF1', 'C57BL/6J', 'C3H/HeJ'],
'AKXD':['AKF1', 'KAF1', 'AKR/J', 'DBA/2J'],
'BXD':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
+'C57BL-6JxC57BL-6NJF2':['', '', 'C57BL/6J', 'C57BL/6NJ'],
'BXD300':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
'B6BTBRF2':['B6BTBRF1', 'BTBRB6F1', 'C57BL/6J', 'BTBRT<+>tf/J'],
'BHHBF2':['B6HF2','HB6F2','C57BL/6J','C3H/HeJ'],
@@ -880,22 +881,6 @@ def cmpGenoPos(A,B):
except:
return 0
-#XZhou: Must use "BINARY" to enable case sensitive comparison.
-def authUser(name,password,db, encrypt=None):
- try:
- if encrypt:
- query = 'SELECT privilege, id,name,password, grpName FROM User WHERE name= BINARY \'%s\' and password= BINARY \'%s\'' % (name,password)
- else:
- query = 'SELECT privilege, id,name,password, grpName FROM User WHERE name= BINARY \'%s\' and password= BINARY SHA(\'%s\')' % (name,password)
- db.execute(query)
- records = db.fetchone()
- if not records:
- raise ValueError
- return records#(privilege,id,name,password,grpName)
- except:
- return (None, None, None, None, None)
-
-
def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users):
access_to_confidential_phenotype_trait = 0
if webqtlConfig.USERDICT[privilege] > webqtlConfig.USERDICT['user']:
diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py
index 07b0b81a..a8363a1f 100755
--- a/wqflask/wqflask/docs.py
+++ b/wqflask/wqflask/docs.py
@@ -8,9 +8,9 @@ class Docs(object):
sql = """
SELECT Docs.title, Docs.content
FROM Docs
- WHERE Docs.entry LIKE '%s'
+ WHERE Docs.entry LIKE %s
"""
- result = g.db.execute(sql % (entry)).fetchone()
+ result = g.db.execute(sql, str(entry)).fetchone()
self.entry = entry
self.title = result[0]
self.content = result[1]
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index bd827086..61305e9b 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -1148,14 +1148,7 @@ class ShowTrait(object):
def make_sample_lists(self, this_trait):
- if self.dataset.group.parlist:
- all_samples_ordered = (self.dataset.group.parlist +
- self.dataset.group.f1list +
- self.dataset.group.samplelist)
- elif self.dataset.group.f1list:
- all_samples_ordered = self.dataset.group.f1list + self.dataset.group.samplelist
- else:
- all_samples_ordered = list(self.dataset.group.samplelist)
+ all_samples_ordered = self.dataset.group.all_samples_ordered()
primary_sample_names = list(all_samples_ordered)
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 12:24:57 +0000