From cd3c99e5f47c529566b05958e79c08e7b85d25c8 Mon Sep 17 00:00:00 2001
From: James Stevenson <james.stevenson@nationwidechildrens.org>
Date: Mon, 8 Jul 2024 09:30:08 -0400
Subject: [PATCH] fix: more logging config fixes (#351)

---
 src/gene/__init__.py | 16 ----------------
 src/gene/query.py    | 18 +++++++++++-------
 2 files changed, 11 insertions(+), 23 deletions(-)

diff --git a/src/gene/__init__.py b/src/gene/__init__.py
index 2c569554..30d1b8c3 100644
--- a/src/gene/__init__.py
+++ b/src/gene/__init__.py
@@ -1,5 +1,4 @@
 """The VICC library for normalizing genes."""
-import logging
 from os import environ
 from pathlib import Path
 
@@ -7,21 +6,6 @@
 
 APP_ROOT = Path(__file__).resolve().parent
 
-logging.basicConfig(
-    filename="gene.log", format="[%(asctime)s] - %(name)s - %(levelname)s : %(message)s"
-)
-logger = logging.getLogger("gene")
-logger.setLevel(logging.DEBUG)
-logger.handlers = []
-
-logging.getLogger("boto3").setLevel(logging.INFO)
-logging.getLogger("botocore").setLevel(logging.INFO)
-logging.getLogger("urllib3").setLevel(logging.INFO)
-logging.getLogger("python_jsonschema_objects").setLevel(logging.INFO)
-logging.getLogger("biocommons.seqrepo.seqaliasdb.seqaliasdb").setLevel(logging.INFO)
-logging.getLogger("biocommons.seqrepo.fastadir.fastadir").setLevel(logging.INFO)
-
-
 SEQREPO_ROOT_DIR = Path(
     environ.get("SEQREPO_ROOT_DIR", "/usr/local/share/seqrepo/latest")
 )
diff --git a/src/gene/query.py b/src/gene/query.py
index e30a79d8..4b81d89d 100644
--- a/src/gene/query.py
+++ b/src/gene/query.py
@@ -1,4 +1,5 @@
 """Provides methods for handling queries."""
+import logging
 import re
 from datetime import datetime
 from typing import Any, Callable, Dict, List, Optional, Set, Tuple, TypeVar
@@ -6,7 +7,7 @@
 from ga4gh.core import core_models, ga4gh_identify
 from ga4gh.vrs import models
 
-from gene import ITEM_TYPES, NAMESPACE_LOOKUP, PREFIX_LOOKUP, logger
+from gene import ITEM_TYPES, NAMESPACE_LOOKUP, PREFIX_LOOKUP
 from gene.database import AbstractDatabase, DatabaseReadException
 from gene.schemas import (
     BaseGene,
@@ -28,6 +29,9 @@
 )
 from gene.version import __version__
 
+
+_logger = logging.getLogger(__name__)
+
 NormService = TypeVar("NormService", bound=BaseNormalizationService)
 
 
@@ -72,7 +76,7 @@ def _emit_warnings(query_str: str) -> List:
                     "non_breaking_space_characters": "Query contains non-breaking space characters"
                 }
             ]
-            logger.warning(
+            _logger.warning(
                 f"Query ({query_str}) contains non-breaking space characters."
             )
         return warnings
@@ -188,14 +192,14 @@ def _fetch_record(
         try:
             match = self.db.get_record_by_id(concept_id, case_sensitive=False)
         except DatabaseReadException as e:
-            logger.error(
+            _logger.error(
                 f"Encountered DatabaseReadException looking up {concept_id}: {e}"
             )
         else:
             if match:
                 self._add_record(response, match, match_type)
             else:
-                logger.error(
+                _logger.error(
                     f"Unable to find expected record for {concept_id} matching as {match_type}"
                 )  # noqa: E501
 
@@ -263,7 +267,7 @@ def _get_search_response(self, query: str, sources: Set[str]) -> Dict:
                             matched_concept_ids.append(ref)
 
             except DatabaseReadException as e:
-                logger.error(
+                _logger.error(
                     f"Encountered DatabaseReadException looking up {item_type}"
                     f" {term}: {e}"
                 )
@@ -535,7 +539,7 @@ def _handle_failed_merge_ref(record: Dict, response: Dict, query: str) -> Dict:
         :param query: original query value
         :return: response with no match
         """
-        logger.error(
+        _logger.error(
             f"Merge ref lookup failed for ref {record['merge_ref']} "
             f"in record {record['concept_id']} from query {query}"
         )
@@ -600,7 +604,7 @@ def _resolve_merge(
             merge = self.db.get_record_by_id(merge_ref, False, True)
             if merge is None:
                 query = response.query
-                logger.error(
+                _logger.error(
                     f"Merge ref lookup failed for ref {record['merge_ref']} "
                     f"in record {record['concept_id']} from query `{query}`"
                 )