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-rwxr-xr-xwqflask/base/data_set.py34
-rwxr-xr-xwqflask/base/webqtlTrait.py15
2 files changed, 26 insertions, 23 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 34e5eaa1..cd9e810e 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -90,9 +90,7 @@ class DataSet(object):
def get_group(self):
- assert self.cursor
- self.cursor.execute(self.query)
- self.group, self.group_id = self.cursor.fetchone()
+ self.group, self.group_id = g.db.execute(self.query).fetchone()
if self.group == 'BXD300':
self.group = "BXD"
#return group
@@ -107,7 +105,7 @@ class DataSet(object):
"""
- query_args = tuple(self.db_conn.escape_string(x) for x in (
+ query_args = tuple(escape(x) for x in (
(self.type + "Freeze"),
str(webqtlConfig.PUBLICTHRESH),
self.name,
@@ -115,18 +113,22 @@ class DataSet(object):
self.name))
print("query_args are:", query_args)
- query = '''
- SELECT
- Id, Name, FullName, ShortName
- FROM
- %s
- WHERE
- public > %s AND
- (Name = "%s" OR FullName = "%s" OR ShortName = "%s")
- ''' % (query_args)
+ print("""
+ SELECT Id, Name, FullName, ShortName
+ FROM %s
+ WHERE public > %s AND
+ (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
+ """ % (query_args))
+
+ self.id, self.name, self.fullname, self.shortname = g.db.execute("""
+ SELECT Id, Name, FullName, ShortName
+ FROM %s
+ WHERE public > %s AND
+ (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
+ """ % (query_args)).fetchone()
- self.cursor.execute(query)
- self.id, self.name, self.fullname, self.shortname = self.cursor.fetchone()
+ #self.cursor.execute(query)
+ #self.id, self.name, self.fullname, self.shortname = self.cursor.fetchone()
#def genHTML(self, Class='c0dd'):
@@ -185,7 +187,7 @@ class PhenotypeDataSet(DataSet):
WHERE
PublishFreeze.InbredSetId = InbredSet.Id AND
PublishFreeze.Name = "%s"
- ''' % self.db_conn.escape_string(self.name)
+ ''' % escape(self.name)
def check_confidentiality(self):
# (Urgently?) Need to write this
diff --git a/wqflask/base/webqtlTrait.py b/wqflask/base/webqtlTrait.py
index 1dceba08..9763e441 100755
--- a/wqflask/base/webqtlTrait.py
+++ b/wqflask/base/webqtlTrait.py
@@ -30,9 +30,9 @@ class webqtlTrait:
self.cellid = kw.get('cellid', None)
self.identification = kw.get('identification', 'un-named trait')
self.group = kw.get('group', None)
- self.haveinfo = kw.get(haveinfo, False)
- self.sequence = kw.get(sequence, None) # Blat sequence, available for ProbeSet
- self.data = kw.get(data, {})
+ self.haveinfo = kw.get('haveinfo', False)
+ self.sequence = kw.get('sequence', None) # Blat sequence, available for ProbeSet
+ self.data = kw.get('data', {})
if kw.get('fullname'):
name2 = value.split("::")
@@ -381,7 +381,7 @@ class webqtlTrait:
# return self.__dict__.items()
def retrieveInfo(self, QTL = None):
- assert self.dataset and self.cursor
+ assert self.dataset
if self.dataset.type == 'Publish':
#self.dataset.DisField = ['Name','PubMed_ID','Phenotype','Abbreviation','Authors','Title',\
# 'Abstract', 'Journal','Volume','Pages','Month','Year','Sequence',\
@@ -434,10 +434,11 @@ class webqtlTrait:
Geno.Name = '%s'
""" % (display_fields_string, self.dataset.name, self.name)
else: #Temp type
- query = 'SELECT %s FROM %s WHERE Name = "%s"' % \
- (string.join(self.dataset.display_fields,','), self.dataset.type, self.name)
-
+ traitInfo = g.db.execute("""SELECT %s FROM %s WHERE Name = '%s'
+ """, (string.join(self.dataset.display_fields,','),
+ self.dataset.type, self.name)).fetchone()
+
self.cursor.execute(query)
traitInfo = self.cursor.fetchone()
if traitInfo: