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authorBonfaceKilz2021-08-06 16:15:17 +0300
committerBonfaceKilz2021-08-13 12:57:50 +0300
commit579ae94b08f0b1cef00350b54dadc12869ad70de (patch)
tree8a660260e60e4915aaf13ab2a60d312684f148ae /wqflask/base/data_set.py
parente2ee1c489f0eb59c3efbf81d42f43a1f74cd1adb (diff)
downloadgenenetwork2-579ae94b08f0b1cef00350b54dadc12869ad70de.tar.gz
base: data_set: Remove unnecessary comments and logging statements
Diffstat (limited to 'wqflask/base/data_set.py')
-rw-r--r--wqflask/base/data_set.py12
1 files changed, 0 insertions, 12 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 4cb82665..edc22540 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -277,7 +277,6 @@ class Markers:
filtered_markers = []
for marker in self.markers:
if marker['name'] in p_values:
- # logger.debug("marker {} IS in p_values".format(i))
marker['p_value'] = p_values[marker['name']]
if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
marker['lod_score'] = 0
@@ -298,7 +297,6 @@ class HumanMarkers(Markers):
self.markers = []
for line in marker_data_fh:
splat = line.strip().split()
- # logger.debug("splat:", splat)
if len(specified_markers) > 0:
if splat[1] in specified_markers:
marker = {}
@@ -737,7 +735,6 @@ class DataSet:
and Strain.SpeciesId=Species.Id
and Species.name = '{}'
""".format(create_in_clause(self.samplelist), *mescape(self.group.species))
- logger.sql(query)
results = dict(g.db.execute(query).fetchall())
sample_ids = [results[item] for item in self.samplelist]
@@ -908,7 +905,6 @@ class PhenotypeDataSet(DataSet):
Geno.Name = '%s' and
Geno.SpeciesId = Species.Id
""" % (species, this_trait.locus)
- logger.sql(query)
result = g.db.execute(query).fetchone()
if result:
@@ -938,7 +934,6 @@ class PhenotypeDataSet(DataSet):
Order BY
Strain.Name
"""
- logger.sql(query)
results = g.db.execute(query, (trait, self.id)).fetchall()
return results
@@ -1005,7 +1000,6 @@ class GenotypeDataSet(DataSet):
Order BY
Strain.Name
"""
- logger.sql(query)
results = g.db.execute(query,
(webqtlDatabaseFunction.retrieve_species_id(self.group.name),
trait, self.name)).fetchall()
@@ -1126,8 +1120,6 @@ class MrnaAssayDataSet(DataSet):
ProbeSet.Name = '%s'
""" % (escape(str(this_trait.dataset.id)),
escape(this_trait.name)))
-
- logger.sql(query)
result = g.db.execute(query).fetchone()
mean = result[0] if result else 0
@@ -1147,7 +1139,6 @@ class MrnaAssayDataSet(DataSet):
Geno.Name = '{}' and
Geno.SpeciesId = Species.Id
""".format(species, this_trait.locus)
- logger.sql(query)
result = g.db.execute(query).fetchone()
if result:
@@ -1179,7 +1170,6 @@ class MrnaAssayDataSet(DataSet):
Order BY
Strain.Name
""" % (escape(trait), escape(self.name))
- logger.sql(query)
results = g.db.execute(query).fetchall()
return results
@@ -1190,7 +1180,6 @@ class MrnaAssayDataSet(DataSet):
where ProbeSetXRef.ProbeSetFreezeId = %s and
ProbeSetXRef.ProbeSetId=ProbeSet.Id;
""" % (column_name, escape(str(self.id)))
- logger.sql(query)
results = g.db.execute(query).fetchall()
return dict(results)
@@ -1224,7 +1213,6 @@ def geno_mrna_confidentiality(ob):
query = '''SELECT Id, Name, FullName, confidentiality,
AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table, ob.name)
- logger.sql(query)
result = g.db.execute(query)
(dataset_id,