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| author | Frederick Muriuki Muriithi | 2023-04-15 19:04:55 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2023-04-15 19:04:55 +0300 |
| commit | 2c517dc9b463f63ffef3c17bd56265b168755c6b (patch) | |
| tree | 312bc0eae282e9125378f044982f3f372862e69a /wqflask | |
| parent | a46ad1d468fe5ace7a4503693e2e4d404f87ebf3 (diff) | |
| download | genenetwork2-2c517dc9b463f63ffef3c17bd56265b168755c6b.tar.gz | |
Revert "Fix the way database_connection() is called"
This reverts commit b8b62aea1c7924e2ee7455c6fe8b34eee7cb8e74.
We do need to decouple the entire `gn3.db_utils` from the
`flask.current_app` object, and as such, the use of `SQL_URI` from the
`utility.tools` module in GN2 was on purpose. This is also to help
towards fixing issue
https://issues.genenetwork.org/issues/bugfix_coupling_current_app_and_db_utils
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/correlation/rust_correlation.py | 14 |
1 files changed, 7 insertions, 7 deletions
diff --git a/wqflask/wqflask/correlation/rust_correlation.py b/wqflask/wqflask/correlation/rust_correlation.py index 097cc45b..67bd5ff5 100644 --- a/wqflask/wqflask/correlation/rust_correlation.py +++ b/wqflask/wqflask/correlation/rust_correlation.py @@ -28,7 +28,7 @@ def query_probes_metadata(dataset, trait_list): if not bool(trait_list) or dataset.type!="ProbeSet": return [] - with database_connection() as conn: + with database_connection(SQL_URI) as conn: with conn.cursor() as cursor: query = """ @@ -98,7 +98,7 @@ def chunk_dataset(dataset, steps, name): ProbeSetXRef.ProbeSetId = ProbeSet.Id """.format(name) - with database_connection() as conn: + with database_connection(SQL_URI) as conn: with conn.cursor() as curr: curr.execute(query) traits_name_dict = dict(curr.fetchall()) @@ -122,7 +122,7 @@ def compute_top_n_sample(start_vars, dataset, trait_list): sample_data=json.loads(samples_vals), dataset_samples=dataset.group.all_samples_ordered()) - with database_connection() as conn: + with database_connection(SQL_URI) as conn: with conn.cursor() as curr: curr.execute( """ @@ -140,7 +140,7 @@ def compute_top_n_sample(start_vars, dataset, trait_list): if len(trait_list) == 0: return {} - with database_connection() as conn: + with database_connection(SQL_URI) as conn: with conn.cursor() as curr: # fetching strain data in bulk query = ( @@ -176,7 +176,7 @@ def compute_top_n_lit(corr_results, target_dataset, this_trait) -> dict: geneid_dict = {trait_name: geneid for (trait_name, geneid) in geneid_dict.items() if corr_results.get(trait_name)} - with database_connection() as conn: + with database_connection(SQL_URI) as conn: return reduce( lambda acc, corr: {**acc, **corr}, compute_all_lit_correlation( @@ -251,7 +251,7 @@ def __compute_sample_corr__( if target_dataset.type == "ProbeSet" and start_vars.get("use_cache") == "true": - with database_connection() as conn: + with database_connection(SQL_URI) as conn: file_path = fetch_text_file(target_dataset.name, conn) if file_path: (sample_vals, target_data) = read_text_file( @@ -338,7 +338,7 @@ def __compute_lit_corr__( (this_trait_geneid, geneid_dict, species) = do_lit_correlation( this_trait, target_dataset) - with database_connection() as conn: + with database_connection(SQL_URI) as conn: return reduce( lambda acc, lit: {**acc, **lit}, compute_all_lit_correlation( |