diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/computations/partial_correlations.py | 2 | ||||
| -rw-r--r-- | gn3/db/partial_correlations.py | 12 | ||||
| -rw-r--r-- | gn3/db/traits.py | 2 | ||||
| -rw-r--r-- | gn3/fs_helpers.py | 5 |
4 files changed, 11 insertions, 10 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"} |