Fix minor issues introduced while fixing linting errors

5 files changed, 29 insertions, 28 deletions

diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py
index f7ddfd0..7110cc5 100644
--- a/gn3/computations/partial_correlations.py
+++ b/gn3/computations/partial_correlations.py
@@ -141,7 +141,7 @@ def find_identical_traits(
         return acc + ident[1]
 
     def __dictify_controls__(acc, control_item):
-        ckey = tuple("{item:.3f}" for item in control_item[0])
+        ckey = tuple(f"{item:.3f}" for item in control_item[0])
         return {**acc, ckey: acc.get(ckey, tuple()) + (control_item[1],)}
 
     return (reduce(## for identical control traits
diff --git a/gn3/db/partial_correlations.py b/gn3/db/partial_correlations.py
index a28b111..72dbf1a 100644
--- a/gn3/db/partial_correlations.py
+++ b/gn3/db/partial_correlations.py
@@ -48,7 +48,7 @@ def temp_traits_data(conn, traits):
         "FROM TempData, Temp, Strain "
         "WHERE TempData.StrainId = Strain.Id "
         "AND TempData.Id = Temp.DataId "
-        "AND Temp.name IN ({', '.join(['%s'] * len(traits))}) "
+        f"AND Temp.name IN ({', '.join(['%s'] * len(traits))}) "
         "ORDER BY Strain.Name")
     with conn.cursor(cursorclass=DictCursor) as cursor:
         cursor.execute(
@@ -386,7 +386,7 @@ def temp_traits_info(
     """
     query = (
         "SELECT Name as trait_name, name, description FROM Temp "
-        "WHERE Name IN ({', '.join(['%s'] * len(traits))})")
+        f"WHERE Name IN ({', '.join(['%s'] * len(traits))})")
     with conn.cursor(cursorclass=DictCursor) as cursor:
         cursor.execute(
             query,
@@ -450,7 +450,7 @@ def publish_datasets_groups(conn: Any, dataset_names: Tuple[str]):
         "InbredSet.Id "
         "FROM InbredSet, PublishFreeze "
         "WHERE PublishFreeze.InbredSetId = InbredSet.Id "
-        "AND PublishFreeze.Name IN ({', '.join(['%s'] * len(dataset_names))})")
+        f"AND PublishFreeze.Name IN ({', '.join(['%s'] * len(dataset_names))})")
     with conn.cursor(cursorclass=DictCursor) as cursor:
         cursor.execute(query, tuple(dataset_names))
         return organise_groups_by_dataset(cursor.fetchall())
@@ -500,7 +500,7 @@ def probeset_datasets_groups(conn, dataset_names):
         "FROM InbredSet, ProbeSetFreeze, ProbeFreeze "
         "WHERE ProbeFreeze.InbredSetId = InbredSet.Id "
         "AND ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId "
-        "AND ProbeSetFreeze.Name IN ({', '.join(['%s'] * len(dataset_names))})")
+        f"AND ProbeSetFreeze.Name IN ({', '.join(['%s'] * len(dataset_names))})")
     with conn.cursor(cursorclass=DictCursor) as cursor:
         cursor.execute(query, tuple(dataset_names))
         return organise_groups_by_dataset(cursor.fetchall())
@@ -547,7 +547,7 @@ def geno_datasets_groups(conn, dataset_names):
         "SELECT GenoFreeze.Name AS dataset_name, InbredSet.Name, InbredSet.Id "
         "FROM InbredSet, GenoFreeze "
         "WHERE GenoFreeze.InbredSetId = InbredSet.Id "
-        "AND GenoFreeze.Name IN ({', '.join(['%s'] * len(dataset_names))})")
+        f"AND GenoFreeze.Name IN ({', '.join(['%s'] * len(dataset_names))})")
     with conn.cursor(cursorclass=DictCursor) as cursor:
         cursor.execute(query, tuple(dataset_names))
         return organise_groups_by_dataset(cursor.fetchall())
@@ -575,7 +575,7 @@ def temp_datasets_groups(conn, dataset_names):
         "SELECT Temp.Name AS dataset_name, InbredSet.Name, InbredSet.Id "
         "FROM InbredSet, Temp "
         "WHERE Temp.InbredSetId = InbredSet.Id "
-        "AND Temp.Name IN ({', '.join(['%s'] * len(dataset_names))})")
+        f"AND Temp.Name IN ({', '.join(['%s'] * len(dataset_names))})")
     with conn.cursor(cursorclass=DictCursor) as cursor:
         cursor.execute(query, tuple(dataset_names))
         return organise_groups_by_dataset(cursor.fetchall())
diff --git a/gn3/db/traits.py b/gn3/db/traits.py
index 90d1e9d..6f979d8 100644
--- a/gn3/db/traits.py
+++ b/gn3/db/traits.py
@@ -402,7 +402,7 @@ def retrieve_probeset_trait_info(trait_data_source: Dict[str, Any], conn: Any):
         "probe_set_note_by_rw", "flag")
     columns = (f"ProbeSet.{x}" for x in keys)
     query = (
-        f"SELECT {','.join(columns)} "
+        f"SELECT {', '.join(columns)} "
         "FROM "
         "ProbeSet, ProbeSetFreeze, ProbeSetXRef "
         "WHERE "
diff --git a/gn3/fs_helpers.py b/gn3/fs_helpers.py
index e2f7ee2..73f6567 100644
--- a/gn3/fs_helpers.py
+++ b/gn3/fs_helpers.py
@@ -71,8 +71,9 @@ contents to TARGET_DIR/<dir-hash>.
             os.mkdir(os.path.join(target_dir, token))
         gzipped_file.save(tar_target_loc)
         # Extract to "tar_target_loc/token"
-        with tarfile.open(tar_target_loc) as tar:
-            tar.extractall(path=os.path.join(target_dir, token))
+        tar = tarfile.open(tar_target_loc)
+        tar.extractall(path=os.path.join(target_dir, token))
+        tar.close()
     # pylint: disable=W0703
     except Exception:
         return {"status": 128, "error": "gzip failed to unpack file"}
diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py
index d7c0b27..de65348 100644
--- a/tests/unit/db/test_traits.py
+++ b/tests/unit/db/test_traits.py
@@ -137,11 +137,10 @@ class TestTraitsDBFunctions(TestCase):
                     "SELECT "
                     "Geno.name, Geno.chr, Geno.mb, Geno.source2, Geno.sequence "
                     "FROM "
-                    "Geno, GenoFreeze, GenoXRef "
+                    "Geno INNER JOIN GenoXRef ON GenoXRef.GenoId = Geno.Id "
+                    "INNER JOIN GenoFreeze ON GenoFreeze.Id = GenoXRef.GenoFreezeId "
                     "WHERE "
-                    "GenoXRef.GenoFreezeId = GenoFreeze.Id "
-                    "AND GenoXRef.GenoId = Geno.Id "
-                    "AND GenoFreeze.Name = %(trait_dataset_name)s "
+                    "GenoFreeze.Name = %(trait_dataset_name)s "
                     "AND Geno.Name = %(trait_name)s"),
                 trait_source)
 
@@ -232,20 +231,21 @@ class TestTraitsDBFunctions(TestCase):
                 error=2.3, count=2),
                              (1, 1, 1))
             cursor.execute.assert_has_calls(
-                [mock.call('SELECT Strain.Id, PublishData.Id FROM'
-                           ' (PublishData, Strain, PublishXRef, '
-                           'PublishFreeze) LEFT JOIN PublishSE ON '
-                           '(PublishSE.DataId = PublishData.Id '
-                           'AND PublishSE.StrainId = '
-                           'PublishData.StrainId) LEFT JOIN NStrain ON '
-                           '(NStrain.DataId = PublishData.Id AND '
-                           'NStrain.StrainId = PublishData.StrainId) WHERE '
-                           'PublishXRef.InbredSetId = '
-                           'PublishFreeze.InbredSetId AND PublishData.Id = '
-                           'PublishXRef.DataId AND PublishXRef.Id = 1 AND '
-                           'PublishXRef.PhenotypeId = 10 AND '
-                           'PublishData.StrainId = Strain.Id AND '
-                           'Strain.Name = "BXD11"'),
+                [mock.call(('SELECT Strain.Id, PublishData.Id FROM'
+                            ' (PublishData, Strain, PublishXRef, '
+                            'PublishFreeze) LEFT JOIN PublishSE ON '
+                            '(PublishSE.DataId = PublishData.Id '
+                            'AND PublishSE.StrainId = '
+                            'PublishData.StrainId) LEFT JOIN NStrain ON '
+                            '(NStrain.DataId = PublishData.Id AND '
+                            'NStrain.StrainId = PublishData.StrainId) WHERE '
+                            'PublishXRef.InbredSetId = '
+                            'PublishFreeze.InbredSetId AND PublishData.Id = '
+                            'PublishXRef.DataId AND PublishXRef.Id = %s AND '
+                            'PublishXRef.PhenotypeId = %s AND '
+                            'PublishData.StrainId = Strain.Id AND '
+                            'Strain.Name = %s'),
+                           ("1", 10, "BXD11")),
                  mock.call(PUBLISH_DATA_SQL, (18.7, 1, 1)),
                  mock.call(PUBLISH_SE_SQL, (2.3, 1, 1)),
                  mock.call(N_STRAIN_SQL, (2, 1, 1))]