diff options
| -rw-r--r-- | gn3/api/correlation.py | 35 | ||||
| -rw-r--r-- | gn3/computations/partial_correlations.py | 8 | ||||
| -rw-r--r-- | gn3/csvcmp.py | 4 | ||||
| -rw-r--r-- | gn3/db/partial_correlations.py | 4 |
4 files changed, 24 insertions, 27 deletions
diff --git a/gn3/api/correlation.py b/gn3/api/correlation.py index aeb7f8c..44aaf56 100644 --- a/gn3/api/correlation.py +++ b/gn3/api/correlation.py @@ -114,13 +114,10 @@ def partial_correlation(): args = request.get_json() with_target_db = args.get("with_target_db", True) - request_errors = None - if with_target_db: - request_errors = __errors__( - args, ("primary_trait", "control_traits", "target_db", "method")) - else: - request_errors = __errors__( - args, ("primary_trait", "control_traits", "target_traits", "method")) + request_errors = __errors__( + args, ("primary_trait", "control_traits", + ("target_db" if with_target_db else "target_traits"), + "method")) if request_errors: return build_response({ "status": "error", @@ -140,15 +137,15 @@ def partial_correlation(): int(args.get("criteria", 500))), job_queue=current_app.config.get("REDIS_JOB_QUEUE"), env = {"PYTHONPATH": ":".join(sys.path), "SQL_URI": SQL_URI})}) - else: - with database_connector() as conn: - results = partial_correlations_with_target_traits( - conn, - trait_fullname(args["primary_trait"]), - tuple( - trait_fullname(trait) for trait in args["control_traits"]), - tuple( - trait_fullname(trait) for trait in args["target_traits"]), - args["method"]) - - return build_response({"status": "success", "results": results}) + + with database_connector() as conn: + results = partial_correlations_with_target_traits( + conn, + trait_fullname(args["primary_trait"]), + tuple( + trait_fullname(trait) for trait in args["control_traits"]), + tuple( + trait_fullname(trait) for trait in args["target_traits"]), + args["method"]) + + return build_response({"status": "success", "results": results}) diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py index 07c73db..9b15bcb 100644 --- a/gn3/computations/partial_correlations.py +++ b/gn3/computations/partial_correlations.py @@ -555,7 +555,7 @@ def trait_for_output(trait): } return {key: val for key, val in trait.items() if val is not None} -def check_for_common_errors( +def check_for_common_errors(# pylint: disable=[R0914] conn, primary_trait_name, control_trait_names, threshold): """Check for common errors""" corr_min_informative = 4 @@ -676,7 +676,7 @@ def partial_correlations_with_target_db(# pylint: disable=[R0913, R0914, R0911] check_res = check_for_common_errors( conn, primary_trait_name, control_trait_names, threshold) if check_res.get("status") == "error": - return error_check_results + return check_res primary_trait = check_res["primary_trait"] input_trait_geneid = primary_trait.get("geneid", 0) @@ -822,12 +822,12 @@ def partial_correlations_with_target_traits( check_res = check_for_common_errors( conn, primary_trait_name, control_trait_names, threshold) if check_res.get("status") == "error": - return error_check_results + return check_res target_traits = { trait["name"]: trait for trait in traits_info(conn, threshold, target_trait_names)} - target_traits_data = traits_data(conn, target_traits.values()) + target_traits_data = traits_data(conn, tuple(target_traits.values())) def __merge(trait, pcorrs): return { diff --git a/gn3/csvcmp.py b/gn3/csvcmp.py index 82d491e..3aba184 100644 --- a/gn3/csvcmp.py +++ b/gn3/csvcmp.py @@ -1,6 +1,6 @@ """This module contains functions for manipulating and working with csv texts""" -from typing import Any, List +from typing import List import re import json @@ -70,7 +70,7 @@ def csv_diff(base_csv, delta_csv, tmp_dir="/tmp") -> dict: base_csv_header, delta_csv_header = line, delta_csv_list[i] break - longest_header = max(base_csv_header, delta_csv_header, key=lambda x: len(x)) + longest_header = max(base_csv_header, delta_csv_header, key=len) if base_csv_header != delta_csv_header: if longest_header != base_csv_header: base_csv = "\n".join([longest_header] + base_csv_list[1:]) diff --git a/gn3/db/partial_correlations.py b/gn3/db/partial_correlations.py index 96f953d..e8466f6 100644 --- a/gn3/db/partial_correlations.py +++ b/gn3/db/partial_correlations.py @@ -9,7 +9,7 @@ This module is part of the optimisation effort for the partial correlations. """ from functools import reduce, partial -from typing import Any, Dict, Tuple, Union, Sequence +from typing import Any, Dict, Tuple, Union, Sequence, Generator from MySQLdb.cursors import DictCursor @@ -750,7 +750,7 @@ def traits_datasets(conn, threshold, traits): def traits_info( conn: Any, threshold: int, traits_fullnames: Tuple[str, ...], - qtl=None) -> Tuple[Dict[str, Any], ...]: + qtl=None) -> Generator: """ Retrieve basic trait information for multiple `traits`. |