diff options
| -rw-r--r-- | wqflask/wqflask/correlation/rust_correlation.py | 27 |
1 files changed, 14 insertions, 13 deletions
diff --git a/wqflask/wqflask/correlation/rust_correlation.py b/wqflask/wqflask/correlation/rust_correlation.py index ef3988e5..92cb362c 100644 --- a/wqflask/wqflask/correlation/rust_correlation.py +++ b/wqflask/wqflask/correlation/rust_correlation.py @@ -134,20 +134,21 @@ def compute_top_n_sample(start_vars, dataset, trait_list): with database_connector() as conn: with conn.cursor() as curr: # fetching strain data in bulk + query = ( + "SELECT * from ProbeSetData " + f"WHERE StrainID IN ({', '.join(['%s'] * len(sample_ids))})" + "AND id IN (" + " SELECT ProbeSetXRef.DataId " + " FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze) " + " WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id " + " AND ProbeSetFreeze.Name = %s " + " AND ProbeSet.Name " + f" IN ({', '.join(['%s'] * len(trait_list))})" + " ProbeSet.Id = ProbeSetXRef.ProbeSetId)" + ")") curr.execute( - """ - SELECT * from ProbeSetData - where StrainID in {} - and id in (SELECT ProbeSetXRef.DataId - FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze) - WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id - and ProbeSetFreeze.Name = '{}' - and ProbeSet.Name in {} - and ProbeSet.Id = ProbeSetXRef.ProbeSetId) - """.format( - create_in_clause(list(sample_ids.values())), - dataset.name, - create_in_clause(trait_list))) + query, + tuple(sample_ids.values()) + (dataset.name,) + tuple(trait_list)) corr_data = chunk_dataset( list(curr.fetchall()), len(sample_ids.values()), dataset.name) |