Fix linting and typing errors

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`.