diff options
| -rw-r--r-- | gn3/api/correlation.py | 16 | ||||
| -rw-r--r-- | gn3/api/heatmaps.py | 20 | ||||
| -rw-r--r-- | gn3/db_utils.py | 4 | ||||
| -rwxr-xr-x | scripts/partial_correlations.py | 26 |
4 files changed, 32 insertions, 34 deletions
diff --git a/gn3/api/correlation.py b/gn3/api/correlation.py index 14c029c..f2ac4d7 100644 --- a/gn3/api/correlation.py +++ b/gn3/api/correlation.py @@ -68,17 +68,15 @@ def compute_lit_corr(species=None, gene_id=None): might be needed for actual computing of the correlation results """ - conn, _cursor_object = database_connector() - target_traits_gene_ids = request.get_json() - target_trait_gene_list = list(target_traits_gene_ids.items()) + with database_connector() as conn: + target_traits_gene_ids = request.get_json() + target_trait_gene_list = list(target_traits_gene_ids.items()) - lit_corr_results = compute_all_lit_correlation( - conn=conn, trait_lists=target_trait_gene_list, - species=species, gene_id=gene_id) + lit_corr_results = compute_all_lit_correlation( + conn=conn, trait_lists=target_trait_gene_list, + species=species, gene_id=gene_id) - conn.close() - - return jsonify(lit_corr_results) + return jsonify(lit_corr_results) @correlation.route("/tissue_corr/<string:corr_method>", methods=["POST"]) diff --git a/gn3/api/heatmaps.py b/gn3/api/heatmaps.py index b2511c3..80c8ca8 100644 --- a/gn3/api/heatmaps.py +++ b/gn3/api/heatmaps.py @@ -24,14 +24,14 @@ def clustered_heatmaps(): return jsonify({ "message": "You need to provide at least two trait names." }), 400 - conn, _cursor = database_connector() - def parse_trait_fullname(trait): - name_parts = trait.split(":") - return f"{name_parts[1]}::{name_parts[0]}" - traits_fullnames = [parse_trait_fullname(trait) for trait in traits_names] + with database_connector() as conn: + def parse_trait_fullname(trait): + name_parts = trait.split(":") + return f"{name_parts[1]}::{name_parts[0]}" + traits_fullnames = [parse_trait_fullname(trait) for trait in traits_names] - with io.StringIO() as io_str: - figure = build_heatmap(traits_fullnames, conn, vertical=vertical) - figure.write_json(io_str) - fig_json = io_str.getvalue() - return fig_json, 200 + with io.StringIO() as io_str: + figure = build_heatmap(traits_fullnames, conn, vertical=vertical) + figure.write_json(io_str) + fig_json = io_str.getvalue() + return fig_json, 200 diff --git a/gn3/db_utils.py b/gn3/db_utils.py index 7263705..3703cbb 100644 --- a/gn3/db_utils.py +++ b/gn3/db_utils.py @@ -14,10 +14,10 @@ def parse_db_url() -> Tuple: parsed_db.password, parsed_db.path[1:]) -def database_connector() -> Tuple: +def database_connector() -> mdb.Connection: """function to create db connector""" host, user, passwd, db_name = parse_db_url() conn = mdb.connect(host, user, passwd, db_name) cursor = conn.cursor() - return (conn, cursor) + return conn diff --git a/scripts/partial_correlations.py b/scripts/partial_correlations.py index ee442df..f203daa 100755 --- a/scripts/partial_correlations.py +++ b/scripts/partial_correlations.py @@ -35,19 +35,19 @@ def cleanup_string(the_str): return the_str.strip('"\t\n\r ') def run_partial_corrs(args): - try: - conn, _cursor_object = database_connector() - return partial_correlations_entry( - conn, cleanup_string(args.primary_trait), - tuple(cleanup_string(args.control_traits).split(",")), - cleanup_string(args.method), args.criteria, - cleanup_string(args.target_database)) - except Exception as exc: - print(traceback.format_exc(), file=sys.stderr) - return { - "status": "exception", - "message": traceback.format_exc() - } + with database_connector() as conn: + try: + return partial_correlations_entry( + conn, cleanup_string(args.primary_trait), + tuple(cleanup_string(args.control_traits).split(",")), + cleanup_string(args.method), args.criteria, + cleanup_string(args.target_database)) + except Exception as exc: + print(traceback.format_exc(), file=sys.stderr) + return { + "status": "exception", + "message": traceback.format_exc() + } def enter(): args = process_cli_arguments() |