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authorPjotr Prins2016-06-23 12:51:12 +0000
committerPjotr Prins2016-06-23 12:51:12 +0000
commit923e94c39f5768f836dbf5fc29b0186c13ccc86b (patch)
tree1269aa252ee1a804386dc2f16f2f60d31779f049
parentf2bbefa47c00ac7344e8172891035a4f82c6d805 (diff)
downloadgenenetwork2-923e94c39f5768f836dbf5fc29b0186c13ccc86b.tar.gz
Logger: SQL
-rw-r--r--wqflask/base/data_set.py8
-rw-r--r--wqflask/base/trait.py12
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py2
3 files changed, 10 insertions, 12 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index a50f5235..ffc5917a 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -1137,7 +1137,7 @@ class TempDataSet(DataSet):
return desc
def get_group(self):
- self.cursor.execute("""
+ query = """
SELECT
InbredSet.Name, InbredSet.Id
FROM
@@ -1145,9 +1145,9 @@ class TempDataSet(DataSet):
WHERE
Temp.InbredSetId = InbredSet.Id AND
Temp.Name = "%s"
- """, self.name)
- self.group, self.group_id = self.cursor.fetchone()
- #return self.group
+ """ % self.name
+ logger.sql(query)
+ self.group, self.group_id = g.db.execute(query).fetchone()
def retrieve_sample_data(self, trait):
query = """
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 4d4d1a42..afde3dbe 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -670,12 +670,12 @@ class GeneralTrait(object):
"""
if self.cellid:
- self.cursor.execute("""
- select ProbeFreeze.Name from ProbeFreeze, ProbeSetFreeze
- where
- ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND
- ProbeSetFreeze.Id = %d""" % thisTrait.dataset.id)
- probeDBName = self.cursor.fetchone()[0]
+ query = """ select ProbeFreeze.Name from ProbeFreeze, ProbeSetFreeze where
+ ProbeFreeze.Id =
+ ProbeSetFreeze.ProbeFreezeId AND
+ ProbeSetFreeze.Id = %d""" % thisTrait.dataset.id
+ logger.sql(query)
+ probeDBName = g.db.execute(query).fetchone()[0]
return dict(name = probeDBName,
url = None)
else:
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 5340301a..3eea3f4a 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -1250,8 +1250,6 @@ def get_nearest_marker(this_trait, this_db):
GenoFreeze.Id = GenoXRef.GenoFreezeId AND
GenoFreeze.Name = '{}'
ORDER BY ABS( Geno.Mb - {}) LIMIT 1""".format(this_chr, this_db.group.name+"Geno", this_mb)
- logger.debug("query:", query)
-
logger.sql(query)
result = g.db.execute(query).fetchall()
logger.debug("result:", result)