fix: Logger suppresion and database logs (#1041)

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

## Description
<!-- Provide a clear description of the changes in this PR -->

## 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.

---------

Co-authored-by: Igor Ilic <30923996+dexters1@users.noreply.github.com>
Co-authored-by: Igor Ilic <igorilic03@gmail.com>

alembic.ini

@@ -102,7 +102,7 @@ handlers =
 qualname = sqlalchemy.engine
 
 [logger_alembic]
-level = INFO
+level = WARN
 handlers =
 qualname = alembic
 

cognee-mcp/entrypoint.sh

@@ -4,6 +4,10 @@ set -e  # Exit on error
 echo "Debug mode: $DEBUG"
 echo "Environment: $ENVIRONMENT"
 
+# Set default transport mode if not specified
+TRANSPORT_MODE=${TRANSPORT_MODE:-"stdio"}
+echo "Transport mode: $TRANSPORT_MODE"
+
 # Run Alembic migrations with proper error handling.
 # Note on UserAlreadyExists error handling:
 # During database migrations, we attempt to create a default user. If this user
@@ -28,19 +32,31 @@ fi
 
 echo "Database migrations done."
 
-echo "Starting Cognee MCP Server..."
+echo "Starting Cognee MCP Server with transport mode: $TRANSPORT_MODE"
 
 # Add startup delay to ensure DB is ready
 sleep 2
 
-# Modified Gunicorn startup with error handling
+# Modified startup with transport mode selection and error handling
 if [ "$ENVIRONMENT" = "dev" ] || [ "$ENVIRONMENT" = "local" ]; then
     if [ "$DEBUG" = "true" ]; then
         echo "Waiting for the debugger to attach..."
-        exec python -m debugpy --wait-for-client --listen 0.0.0.0:5678 -m cognee
+        if [ "$TRANSPORT_MODE" = "sse" ]; then
+            exec python -m debugpy --wait-for-client --listen 0.0.0.0:5678 -m cognee --transport sse
+        else
+            exec python -m debugpy --wait-for-client --listen 0.0.0.0:5678 -m cognee --transport stdio
+        fi
     else
-        exec cognee
+        if [ "$TRANSPORT_MODE" = "sse" ]; then
+            exec cognee --transport sse
+        else
+            exec cognee --transport stdio
+        fi
     fi
 else
-    exec cognee
+    if [ "$TRANSPORT_MODE" = "sse" ]; then
+        exec cognee --transport sse
+    else
+        exec cognee --transport stdio
+    fi
 fi

cognee-mcp/src/server.py

@@ -18,6 +18,7 @@ from cognee.modules.search.types import SearchType
 from cognee.shared.data_models import KnowledgeGraph
 from cognee.modules.storage.utils import JSONEncoder
 
+
 try:
     from codingagents.coding_rule_associations import (
         add_rule_associations,

cognee/infrastructure/llm/gemini/adapter.py

@@ -1,4 +1,5 @@
 import litellm
+import logging
 from pydantic import BaseModel
 from typing import Type, Optional
 from litellm import acompletion, JSONSchemaValidationError

cognee/infrastructure/llm/generic_llm_api/adapter.py

@@ -1,5 +1,6 @@
 """Adapter for Generic API LLM provider API"""
 
+import logging
 from typing import Type
 
 from pydantic import BaseModel
@@ -7,6 +8,7 @@ import instructor
 from cognee.infrastructure.llm.llm_interface import LLMInterface
 from cognee.infrastructure.llm.config import get_llm_config
 from cognee.infrastructure.llm.rate_limiter import rate_limit_async, sleep_and_retry_async
+from cognee.shared.logging_utils import get_logger
 import litellm
 
 

cognee/infrastructure/llm/utils.py

@@ -1,8 +1,7 @@
-from cognee.shared.logging_utils import get_logger
 import litellm
 
-from cognee.infrastructure.databases.vector import get_vector_engine
 from cognee.infrastructure.llm.get_llm_client import get_llm_client
+from cognee.shared.logging_utils import get_logger
 
 logger = get_logger()
 
@@ -22,6 +21,9 @@ def get_max_chunk_tokens():
           the smaller value of the embedding engine's max tokens and half of the LLM's
           maximum tokens.
     """
+    # NOTE: Import must be done in function to avoid circular import issue
+    from cognee.infrastructure.databases.vector import get_vector_engine
+
     # Calculate max chunk size based on the following formula
     embedding_engine = get_vector_engine().embedding_engine
     llm_client = get_llm_client()
@@ -93,6 +95,9 @@ async def test_embedding_connection():
     the exception if the connection to the embedding handler cannot be established.
     """
     try:
+        # NOTE: Vector engine import must be done in function to avoid circular import issue
+        from cognee.infrastructure.databases.vector import get_vector_engine
+
         await get_vector_engine().embedding_engine.embed_text("test")
     except Exception as e:
         logger.error(e)

cognee/modules/data/processing/document_types/open_data_file.py

@@ -1,4 +1,6 @@
 from typing import IO, Optional
+from urllib.parse import urlparse
+import os
 from cognee.api.v1.add.config import get_s3_config
 
 
@@ -24,8 +26,16 @@ def open_data_file(
         else:
             return fs.open(file_path, mode=mode, encoding=encoding, **kwargs)
     elif file_path.startswith("file://"):
-        # Handle local file URLs by stripping the file:// prefix
+        # Handle local file URLs by properly parsing the URI
-        file_path = file_path.replace("file://", "", 1)
+        parsed_url = urlparse(file_path)
-        return open(file_path, mode=mode, encoding=encoding, **kwargs)
+        # On Windows, urlparse handles drive letters correctly
+        # Convert the path component to a proper file path
+        if os.name == "nt":  # Windows
+            # Remove leading slash from Windows paths like /C:/Users/...
+            local_path = parsed_url.path.lstrip("/")
+        else:  # Unix-like systems
+            local_path = parsed_url.path
+
+        return open(local_path, mode=mode, encoding=encoding, **kwargs)
     else:
         return open(file_path, mode=mode, encoding=encoding, **kwargs)

cognee/shared/logging_utils.py

@@ -11,6 +11,23 @@ import importlib.metadata
 from cognee import __version__ as cognee_version
 from typing import Protocol
 
+
+# Configure external library logging
+def configure_external_library_logging():
+    """Configure logging for external libraries to reduce verbosity"""
+    # Configure LiteLLM logging to reduce verbosity
+    try:
+        import litellm
+
+        litellm.set_verbose = False
+
+        # Suppress LiteLLM ERROR logging using standard logging
+        logging.getLogger("litellm").setLevel(logging.CRITICAL)
+    except ImportError:
+        # LiteLLM not available, skip configuration
+        pass
+
+
 # Export common log levels
 DEBUG = logging.DEBUG
 INFO = logging.INFO
@@ -148,6 +165,44 @@ def get_logger(name=None, level=None) -> LoggerInterface:
         return logger
 
 
+def log_database_configuration(logger):
+    """Log the current database configuration for all database types"""
+    # NOTE: Has to be imporated at runtime to avoid circular import
+    from cognee.infrastructure.databases.relational.config import get_relational_config
+    from cognee.infrastructure.databases.vector.config import get_vectordb_config
+    from cognee.infrastructure.databases.graph.config import get_graph_config
+
+    try:
+        # Log relational database configuration
+        relational_config = get_relational_config()
+        logger.info(f"Relational database: {relational_config.db_provider}")
+        if relational_config.db_provider == "postgres":
+            logger.info(f"Postgres host: {relational_config.db_host}:{relational_config.db_port}")
+            logger.info(f"Postgres database: {relational_config.db_name}")
+        elif relational_config.db_provider == "sqlite":
+            logger.info(f"SQLite path: {relational_config.db_path}")
+            logger.info(f"SQLite database: {relational_config.db_name}")
+
+        # Log vector database configuration
+        vector_config = get_vectordb_config()
+        logger.info(f"Vector database: {vector_config.vector_db_provider}")
+        if vector_config.vector_db_provider == "lancedb":
+            logger.info(f"Vector database path: {vector_config.vector_db_url}")
+        else:
+            logger.info(f"Vector database URL: {vector_config.vector_db_url}")
+
+        # Log graph database configuration
+        graph_config = get_graph_config()
+        logger.info(f"Graph database: {graph_config.graph_database_provider}")
+        if graph_config.graph_database_provider == "kuzu":
+            logger.info(f"Graph database path: {graph_config.graph_file_path}")
+        else:
+            logger.info(f"Graph database URL: {graph_config.graph_database_url}")
+
+    except Exception as e:
+        logger.warning(f"Could not retrieve database configuration: {str(e)}")
+
+
 def cleanup_old_logs(logs_dir, max_files):
     """
     Removes old log files, keeping only the most recent ones.
@@ -193,6 +248,9 @@ def setup_logging(log_level=None, name=None):
 
     log_level = log_level if log_level else log_levels[os.getenv("LOG_LEVEL", "INFO")]
 
+    # Configure external library logging early to suppress verbose output
+    configure_external_library_logging()
+
     def exception_handler(logger, method_name, event_dict):
         """Custom processor to handle uncaught exceptions."""
         # Check if there's an exc_info that needs to be processed
@@ -339,6 +397,9 @@ def setup_logging(log_level=None, name=None):
 
     logger.info("Want to learn more? Visit the Cognee documentation: https://docs.cognee.ai")
 
+    # Log database configuration
+    log_database_configuration(logger)
+
     # Return the configured logger
     return logger
 

cognee/tests/unit/modules/data/test_open_data_file.py

@@ -1,6 +1,7 @@
 import os
 import tempfile
 import pytest
+from pathlib import Path
 from cognee.modules.data.processing.document_types.open_data_file import open_data_file
 
 
@@ -29,7 +30,8 @@ class TestOpenDataFile:
             temp_file_path = f.name
 
         try:
-            file_url = f"file://{temp_file_path}"
+            # Use pathlib.Path.as_uri() for proper cross-platform file URL creation
+            file_url = Path(temp_file_path).as_uri()
             with open_data_file(file_url, mode="r") as f:
                 content = f.read()
                 assert content == test_content
@@ -44,7 +46,8 @@ class TestOpenDataFile:
             temp_file_path = f.name
 
         try:
-            file_url = f"file://{temp_file_path}"
+            # Use pathlib.Path.as_uri() for proper cross-platform file URL creation
+            file_url = Path(temp_file_path).as_uri()
             with open_data_file(file_url, mode="rb") as f:
                 content = f.read()
                 assert content == test_content.encode()
@@ -61,7 +64,8 @@ class TestOpenDataFile:
             temp_file_path = f.name
 
         try:
-            file_url = f"file://{temp_file_path}"
+            # Use pathlib.Path.as_uri() for proper cross-platform file URL creation
+            file_url = Path(temp_file_path).as_uri()
             with open_data_file(file_url, mode="r", encoding="utf-8") as f:
                 content = f.read()
                 assert content == test_content
@@ -84,7 +88,9 @@ class TestOpenDataFile:
 
         try:
             # Even if someone accidentally adds multiple file:// prefixes
-            file_url = f"file://file://{temp_file_path}"
+            # Use proper file URL creation first
+            proper_file_url = Path(temp_file_path).as_uri()
+            file_url = f"file://{proper_file_url}"
             with open_data_file(file_url, mode="r") as f:
                 content = f.read()
                 # This should work because we only replace the first occurrence