Jspv structlog auto config fix (#907)

<!-- .github/pull_request_template.md -->

## Description
PR from user jspv, running it through our branch to test CI/CD

## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin.

---------

Signed-off-by: Diego B Theuerkauf <diego.theuerkauf@tuebingen.mpg.de>
Co-authored-by: Boris <boris@topoteretes.com>
Co-authored-by: vasilije <vas.markovic@gmail.com>
Co-authored-by: Vasilije <8619304+Vasilije1990@users.noreply.github.com>
Co-authored-by: Hande <159312713+hande-k@users.noreply.github.com>
Co-authored-by: Matea Pesic <80577904+matea16@users.noreply.github.com>
Co-authored-by: hajdul88 <52442977+hajdul88@users.noreply.github.com>
Co-authored-by: Daniel Molnar <soobrosa@gmail.com>
Co-authored-by: Diego Baptista Theuerkauf <34717973+diegoabt@users.noreply.github.com>
Co-authored-by: Dmitrii Galkin <36552323+dm1tryG@users.noreply.github.com>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Co-authored-by: lxobr <122801072+lxobr@users.noreply.github.com>
Co-authored-by: github-actions[bot] <github-actions@users.noreply.github.com>
Co-authored-by: jspv <jspvgithub@twinleaf.xyz>

cognee-mcp/src/server.py

@@ -4,7 +4,7 @@ import sys
 import argparse
 import cognee
 import asyncio
-from cognee.shared.logging_utils import get_logger, get_log_file_location
+from cognee.shared.logging_utils import get_logger, setup_logging, get_log_file_location
 import importlib.util
 from contextlib import redirect_stdout
 import mcp.types as types
@@ -20,7 +20,6 @@ from cognee.modules.storage.utils import JSONEncoder
 mcp = FastMCP("Cognee")
 
 logger = get_logger()
-log_file = get_log_file_location()
 
 
 @mcp.tool()
@@ -91,7 +90,7 @@ async def cognee_add_developer_rules(
             tasks.append(asyncio.create_task(cognify_task(abs_path)))
         else:
             logger.warning(f"Skipped missing developer rule file: {abs_path}")
-
+    log_file = get_log_file_location()
     return [
         types.TextContent(
             type="text",
@@ -173,6 +172,7 @@ async def cognify(data: str, graph_model_file: str = None, graph_model_name: str
         )
     )
 
+    log_file = get_log_file_location()
     text = (
         f"Background process launched due to MCP timeout limitations.\n"
         f"To check current cognify status use the cognify_status tool\n"
@@ -234,6 +234,7 @@ async def codify(repo_path: str) -> list:
 
     asyncio.create_task(codify_task(repo_path))
 
+    log_file = get_log_file_location()
     text = (
         f"Background process launched due to MCP timeout limitations.\n"
         f"To check current codify status use the codify_status tool\n"
@@ -454,6 +455,8 @@ async def main():
 
 
 if __name__ == "__main__":
+    logger = setup_logging()
+
     try:
         asyncio.run(main())
     except Exception as e:

cognee/__init__.py

@@ -1,9 +1,20 @@
+# ruff: noqa: E402
 from cognee.version import get_cognee_version
 
 # NOTE: __version__ extraction must be at the top of the __init__.py otherwise
 #       there will be circular import issues
 __version__ = get_cognee_version()
 
+# Load environment variable settings has to be before setting up logging for LOG_LEVEL value
+import dotenv
+
+dotenv.load_dotenv(override=True)
+
+# NOTE: Log level can be set with the LOG_LEVEL env variable
+from cognee.shared.logging_utils import setup_logging
+
+logger = setup_logging()
+
 from .api.v1.add import add
 from .api.v1.delete import delete
 from .api.v1.cognify import cognify
@@ -18,7 +29,3 @@ from cognee.modules.visualization.cognee_network_visualization import (
 
 # Pipelines
 from .modules import pipelines
-
-import dotenv
-
-dotenv.load_dotenv(override=True)

cognee/api/client.py

@@ -3,7 +3,7 @@
 import os
 
 import uvicorn
-from cognee.shared.logging_utils import get_logger
+from cognee.shared.logging_utils import get_logger, setup_logging
 import sentry_sdk
 from fastapi import FastAPI, status
 from fastapi.responses import JSONResponse, Response
@@ -195,4 +195,5 @@ def start_api_server(host: str = "0.0.0.0", port: int = 8000):
 
 
 if __name__ == "__main__":
+    logger = setup_logging()
     start_api_server()

cognee/api/v1/cognify/code_graph_pipeline.py

@@ -2,7 +2,7 @@ import os
 import pathlib
 import asyncio
 from uuid import NAMESPACE_OID, uuid5
-from cognee.shared.logging_utils import get_logger
+from cognee.shared.logging_utils import get_logger, setup_logging
 from cognee.modules.observability.get_observe import get_observe
 
 from cognee.api.v1.search import SearchType, search
@@ -97,4 +97,5 @@ if __name__ == "__main__":
         for file in search_results:
             print(file["name"])
 
+    logger = setup_logging(name="code_graph_pipeline")
     asyncio.run(main())

cognee/api/v1/visualize/visualize.py

@@ -2,7 +2,7 @@ from cognee.modules.visualization.cognee_network_visualization import (
     cognee_network_visualization,
 )
 from cognee.infrastructure.databases.graph import get_graph_engine
-from cognee.shared.logging_utils import get_logger, ERROR
+from cognee.shared.logging_utils import get_logger, setup_logging, ERROR
 
 
 import asyncio
@@ -28,7 +28,7 @@ async def visualize_graph(destination_file_path: str = None):
 
 
 if __name__ == "__main__":
-    logger = get_logger(level=ERROR)
+    logger = setup_logging(log_level=ERROR)
     loop = asyncio.new_event_loop()
     asyncio.set_event_loop(loop)
     try:

cognee/modules/retrieval/utils/description_to_codepart_search.py

@@ -1,5 +1,5 @@
 import asyncio
-from cognee.shared.logging_utils import get_logger, ERROR
+from cognee.shared.logging_utils import get_logger, setup_logging, ERROR
 
 from typing import List
 from cognee.infrastructure.databases.graph import get_graph_engine
@@ -144,6 +144,7 @@ async def code_description_to_code_part(
 
 
 if __name__ == "__main__":
+    logger = setup_logging(log_level=ERROR)
 
     async def main():
         query = "I am looking for a class with blue eyes"

cognee/shared/logging_utils.py

@@ -1,6 +1,5 @@
 import os
 import sys
-import threading
 import logging
 import structlog
 import traceback
@@ -10,6 +9,7 @@ from pathlib import Path
 import importlib.metadata
 
 from cognee import __version__ as cognee_version
+from typing import Protocol
 
 # Export common log levels
 DEBUG = logging.DEBUG
@@ -27,11 +27,8 @@ log_levels = {
     "NOTSET": logging.NOTSET,
 }
 
-# Track if logging has been configured
+# Track if structlog logging has been configured
-_is_configured = False
+_is_structlog_configured = False
-
-# Create a lock for thread-safe initialization
-_setup_lock = threading.Lock()
 
 # Path to logs directory
 LOGS_DIR = Path(os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(__file__))), "logs"))
@@ -128,45 +125,27 @@ class PlainFileHandler(logging.FileHandler):
             self.flush()
 
 
-class LoggerInterface:
+class LoggerInterface(Protocol):
-    def info(self, msg, *args, **kwargs):
+    def info(self, msg: str, *args, **kwargs) -> None: ...
-        pass
+    def warning(self, msg: str, *args, **kwargs) -> None: ...
-
+    def error(self, msg: str, *args, **kwargs) -> None: ...
-    def warning(self, msg, *args, **kwargs):
+    def critical(self, msg: str, *args, **kwargs) -> None: ...
-        pass
+    def debug(self, msg: str, *args, **kwargs) -> None: ...
-
-    def error(self, msg, *args, **kwargs):
-        pass
-
-    def critical(self, msg, *args, **kwargs):
-        pass
-
-    def debug(self, msg, *args, **kwargs):
-        pass
 
 
 def get_logger(name=None, level=None) -> LoggerInterface:
-    """Get a configured structlog logger.
+    """Get a logger.
 
-    Args:
+    If `setup_logging()` has not been called, returns a standard Python logger.
-        name: Logger name (default: None, uses __name__)
+    If `setup_logging()` has been called, returns a structlog logger.
-        level: Logging level (default: None)
-
-    Returns:
-        A configured structlog logger instance
     """
-    global _is_configured
+    if _is_structlog_configured:
-
+        return structlog.get_logger(name if name else __name__)
-    # Always first check if logger is already configured to not use threading lock if not necessary
+    else:
-    if not _is_configured:
+        logger = logging.getLogger(name if name else __name__)
-        # Use threading lock to make sure setup_logging can be called only once
+        if level is not None:
-        with _setup_lock:
+            logger.setLevel(level)
-            # Unfortunately we also need a second check in case lock was entered twice at the same time
+        return logger
-            if not _is_configured:
-                setup_logging(level)
-                _is_configured = True
-
-    return structlog.get_logger(name if name else __name__)
 
 
 def cleanup_old_logs(logs_dir, max_files):
@@ -177,9 +156,8 @@ def cleanup_old_logs(logs_dir, max_files):
         logs_dir: Directory containing log files
         max_files: Maximum number of log files to keep
     """
+    logger = structlog.get_logger()
     try:
-        logger = structlog.get_logger()
-
         # Get all .log files in the directory (excluding README and other files)
         log_files = [f for f in logs_dir.glob("*.log") if f.is_file()]
 
@@ -211,6 +189,7 @@ def setup_logging(log_level=None, name=None):
     Returns:
         A configured structlog logger instance
     """
+    global _is_structlog_configured
 
     log_level = log_level if log_level else log_levels[os.getenv("LOG_LEVEL", "INFO")]
 
@@ -260,9 +239,11 @@ def setup_logging(log_level=None, name=None):
 
         logger = structlog.get_logger()
         logger.error(
-            "Uncaught exception",
+            "Exception",
             exc_info=(exc_type, exc_value, traceback),
         )
+        # Hand back to the original hook → prints traceback and exits
+        sys.__excepthook__(exc_type, exc_value, traceback)
 
     # Install exception handlers
     sys.excepthook = handle_exception
@@ -325,6 +306,7 @@ def setup_logging(log_level=None, name=None):
 
     if log_level > logging.DEBUG:
         import warnings
+
         from sqlalchemy.exc import SAWarning
 
         warnings.filterwarnings(
@@ -337,6 +319,9 @@ def setup_logging(log_level=None, name=None):
     # Clean up old log files, keeping only the most recent ones
     cleanup_old_logs(LOGS_DIR, MAX_LOG_FILES)
 
+    # Mark logging as configured
+    _is_structlog_configured = True
+
     # Get a configured logger and log system information
     logger = structlog.get_logger(name if name else __name__)
     logger.info(
@@ -352,7 +337,7 @@ def setup_logging(log_level=None, name=None):
 
 
 def get_log_file_location():
-    # Get the root logger
+    """Return the file path of the log file in use, if any."""
     root_logger = logging.getLogger()
 
     # Loop through handlers to find the FileHandler

examples/python/code_graph_example.py

@@ -2,7 +2,7 @@ import argparse
 import asyncio
 import cognee
 from cognee import SearchType
-from cognee.shared.logging_utils import get_logger, ERROR
+from cognee.shared.logging_utils import setup_logging, ERROR
 
 from cognee.api.v1.cognify.code_graph_pipeline import run_code_graph_pipeline
 
@@ -41,7 +41,7 @@ def parse_args():
 
 
 if __name__ == "__main__":
-    logger = get_logger(level=ERROR)
+    logger = setup_logging(log_level=ERROR)
 
     args = parse_args()
 

examples/python/dynamic_steps_example.py

@@ -1,8 +1,8 @@
-import cognee
 import asyncio
-from cognee.shared.logging_utils import get_logger, ERROR
 
+import cognee
 from cognee.api.v1.search import SearchType
+from cognee.shared.logging_utils import setup_logging, ERROR
 
 job_1 = """
 CV 1: Relevant
@@ -191,7 +191,7 @@ async def main(enable_steps):
 
 
 if __name__ == "__main__":
-    logger = get_logger(level=ERROR)
+    logger = setup_logging(log_level=ERROR)
 
     rebuild_kg = True
     retrieve = True

examples/python/graphiti_example.py

@@ -1,7 +1,7 @@
 import asyncio
 
 import cognee
-from cognee.shared.logging_utils import get_logger, ERROR
+from cognee.shared.logging_utils import setup_logging, ERROR
 from cognee.modules.pipelines import Task, run_tasks
 from cognee.tasks.temporal_awareness import build_graph_with_temporal_awareness
 from cognee.infrastructure.databases.relational import (
@@ -74,7 +74,7 @@ async def main():
 
 
 if __name__ == "__main__":
-    logger = get_logger(level=ERROR)
+    logger = setup_logging(log_level=ERROR)
     loop = asyncio.new_event_loop()
     asyncio.set_event_loop(loop)
     try:

examples/python/multimedia_example.py

@@ -1,7 +1,7 @@
 import os
 import asyncio
 import pathlib
-from cognee.shared.logging_utils import get_logger, ERROR
+from cognee.shared.logging_utils import setup_logging, ERROR
 
 import cognee
 from cognee.api.v1.search import SearchType
@@ -46,7 +46,7 @@ async def main():
 
 
 if __name__ == "__main__":
-    logger = get_logger(level=ERROR)
+    logger = setup_logging(log_level=ERROR)
     loop = asyncio.new_event_loop()
     asyncio.set_event_loop(loop)
     try:

examples/python/ontology_demo_example.py

@@ -1,11 +1,10 @@
-import cognee
 import asyncio
-from cognee.shared.logging_utils import get_logger
 import os
 
+import cognee
 from cognee.api.v1.search import SearchType
 from cognee.api.v1.visualize.visualize import visualize_graph
-
+from cognee.shared.logging_utils import setup_logging
 
 text_1 = """
 1. Audi
@@ -75,7 +74,7 @@ async def main():
 
 
 if __name__ == "__main__":
-    logger = get_logger()
+    logger = setup_logging()
 
     loop = asyncio.new_event_loop()
     asyncio.set_event_loop(loop)

examples/python/ontology_demo_example_2.py

@@ -1,6 +1,6 @@
 import cognee
 import asyncio
-from cognee.shared.logging_utils import get_logger
+from cognee.shared.logging_utils import setup_logging
 import os
 import textwrap
 from cognee.api.v1.search import SearchType
@@ -92,7 +92,7 @@ async def main():
 
 
 if __name__ == "__main__":
-    logger = get_logger()
+    logger = setup_logging()
 
     loop = asyncio.new_event_loop()
     asyncio.set_event_loop(loop)

examples/python/simple_example.py

@@ -1,6 +1,6 @@
 import asyncio
 import cognee
-from cognee.shared.logging_utils import get_logger, ERROR
+from cognee.shared.logging_utils import setup_logging, ERROR
 from cognee.api.v1.search import SearchType
 
 # Prerequisites:
@@ -67,7 +67,7 @@ async def main():
 
 
 if __name__ == "__main__":
-    logger = get_logger(level=ERROR)
+    logger = setup_logging(log_level=ERROR)
     loop = asyncio.new_event_loop()
     asyncio.set_event_loop(loop)
     try:

examples/python/simple_node_set_example.py

@@ -2,7 +2,7 @@ import os
 import asyncio
 import cognee
 from cognee.api.v1.visualize.visualize import visualize_graph
-from cognee.shared.logging_utils import get_logger, ERROR
+from cognee.shared.logging_utils import setup_logging, ERROR
 
 text_a = """
     AI is revolutionizing financial services through intelligent fraud detection
@@ -39,6 +39,6 @@ async def main():
 
 
 if __name__ == "__main__":
-    logger = get_logger(level=ERROR)
+    logger = setup_logging(log_level=ERROR)
     loop = asyncio.new_event_loop()
     asyncio.run(main())