Feat/ss otel context propagation

pyproject.toml

@@ -18,7 +18,11 @@ classifiers = [
 ]
 authors = [{ name = "vvcb" }, { name = "shen1802" }, { name = "nikomoegre" }]
 requires-python = ">=3.13"
-dependencies = ["ibis-framework[duckdb]>=10.5.0", "mcp[cli]>=1.6.0"]
+dependencies = [
+    "ibis-framework[duckdb]>=10.5.0",
+ "langfuse>=3.5.2",
+ "mcp[cli]>=1.6.0",
+]
 urls = { Documentation = "https://fastomop.github.io/omcp/", Repository = "https://github.com/fastomop/omcp" }
 
 [project.scripts]

sample.env

@@ -1,47 +1,110 @@
-# Database Configuration
+# OMOP MCP Server Configuration Template
+# Copy this file to .env and modify the values according to your setup
+
+# ============================================================================
+# LOGGING AND OBSERVABILITY CONFIGURATION
+# ============================================================================
+
+# Enable/disable file logging (default: true)
+# Set to false to disable all logging output
+ENABLE_LOGGING=true
+DEBUG=false
+LOG_FILE=omcp.log
+
+# Enable/disable Langfuse observability and tracing (default: true)
+# Set to false to disable Langfuse integration
+ENABLE_LANGFUSE=true
+
+
+# ============================================================================
+# LANGFUSE CONFIGURATION
+# ============================================================================
+
+# Langfuse public and secret keys
+# Get these from your Langfuse project settings
+LANGFUSE_PUBLIC_KEY="pk-lf-your-public-key-here"
+LANGFUSE_SECRET_KEY="sk-lf-your-secret-key-here"
+
+# Langfuse host URL
+# Use https://cloud.langfuse.com for Langfuse Cloud
+# Use http://localhost:3000 for self-hosted Langfuse
+LANGFUSE_HOST="https://cloud.langfuse.com"
+
+# Trace context file for distributed tracing (optional)
+# Used for linking traces between fastomop and omcp across processes
+# Default: Uses system temp directory (e.g., /tmp/ on Unix, %TEMP% on Windows)
+# Only set this if you need a custom location or for cross-service coordination
+#LANGFUSE_TRACE_CONTEXT_FILE=/tmp/.fastomop_langfuse_trace_context.json
+
+# ============================================================================
+# DATABASE CONFIGURATION
+# ============================================================================
+
 # Supported database types: duckdb, postgres
 DB_TYPE=duckdb
-#DB_TYPE=postgres
-
-# DuckDB Configuration (when DB_TYPE=duckdb)
-# Database Path (for DuckDB)
-DB_PATH=/path/to/omcp/synthetic_data/synthea.duckdb
 
 # Database Read-Only Mode (recommended for production)
 # Set to true to prevent accidental database modifications
 DB_READ_ONLY=true
 
-# PostgreSQL Configuration (when DB_TYPE=postgres)
-#DB_USERNAME=your_username
-#DB_PASSWORD=your_password
-#DB_HOST=localhost
-#DB_PORT=5432
-#DB_DATABASE=your_database_name
+# ============================================================================
+# DUCKDB CONFIGURATION (when DB_TYPE=duckdb)
+# ============================================================================
+
+# Path to your DuckDB database file
+DB_PATH=/path/to/your/omop.duckdb
+
+# ============================================================================
+# POSTGRESQL CONFIGURATION (when DB_TYPE=postgres)
+# ============================================================================
+
+# PostgreSQL connection details
+DB_USERNAME=your_username
+DB_PASSWORD=your_password
+DB_HOST=localhost
+DB_PORT=5432
+DB_DATABASE=your_database_name
+
+# ============================================================================
+# OMOP SCHEMA CONFIGURATION
+# ============================================================================
+
+# Schema containing OMOP CDM tables
+CDM_SCHEMA=cdm
 
-# OMOP Schema Configuration
-CDM_SCHEMA=base    # Schema containing OMOP CDM tables
-VOCAB_SCHEMA=base  # Schema containing vocabulary tables
+# Schema containing vocabulary tables (can be same as CDM_SCHEMA)
+VOCAB_SCHEMA=vocab
+
+# ============================================================================
+# MCP SERVER CONFIGURATION
+# ============================================================================
 
-# MCP Server Configuration (optional)
 # Transport type:
 #   - stdio: For direct integration with MCP clients (Claude Desktop, etc.)
 #   - sse: For web-based clients and HTTP API access
 MCP_TRANSPORT=stdio
 
 # Host and port configuration (required for SSE transport, ignored for stdio)
-#MCP_HOST=localhost
-#MCP_PORT=8080
+MCP_HOST=localhost
+MCP_PORT=8080
 
-# Example Configurations:
+# ============================================================================
+# EXAMPLE CONFIGURATIONS
+# ============================================================================
 
-# DuckDB Example (Local file database)
+# Example 1: DuckDB with full logging
+#ENABLE_LOGGING=true
+#ENABLE_LANGFUSE=true
 #DB_TYPE=duckdb
 #DB_PATH=/Users/username/data/omop.duckdb
 #DB_READ_ONLY=true
 #CDM_SCHEMA=cdm
 #VOCAB_SCHEMA=vocab
+#MCP_TRANSPORT=stdio
 
-# PostgreSQL Example (Remote database)
+# Example 2: PostgreSQL with minimal logging
+#ENABLE_LOGGING=true
+#ENABLE_LANGFUSE=false
 #DB_TYPE=postgres
 #DB_USERNAME=omop_user
 #DB_PASSWORD=secure_password
@@ -51,3 +114,16 @@ MCP_TRANSPORT=stdio
 #DB_READ_ONLY=true
 #CDM_SCHEMA=cdm_531
 #VOCAB_SCHEMA=vocab
+#MCP_TRANSPORT=sse
+#MCP_HOST=0.0.0.0
+#MCP_PORT=8080
+
+# Example 3: Development setup with no logging
+#ENABLE_LOGGING=false
+#ENABLE_LANGFUSE=false
+#DB_TYPE=duckdb
+#DB_PATH=/tmp/test.duckdb
+#DB_READ_ONLY=false
+#CDM_SCHEMA=main
+#VOCAB_SCHEMA=main
+#MCP_TRANSPORT=stdio

src/omcp/config.py

@@ -0,0 +1,79 @@
+import os
+import logging
+from pathlib import Path
+from dotenv import load_dotenv
+from langfuse import Langfuse
+from langfuse import observe
+
+load_dotenv()
+
+# Global configuration variables
+ENABLE_LOGGING = os.environ.get("ENABLE_LOGGING", "true").lower() == "true"
+ENABLE_LANGFUSE = os.environ.get("ENABLE_LANGFUSE", "true").lower() == "true"
+
+
+def setup_logging():
+    """Set up simplified logging configuration."""
+    logger = logging.getLogger("omcp")
+
+    if not ENABLE_LOGGING:
+        logger.addHandler(logging.NullHandler())
+        return logger
+
+    # Clear existing handlers
+    logger.handlers.clear()
+    logger.setLevel(logging.INFO)
+
+    # Get log file path (simplified)
+    log_file = os.environ.get("LOG_FILE", "omcp.log")
+    if not os.path.isabs(log_file):
+        # Default to home directory logs folder
+        log_dir = Path.home() / ".omcp" / "logs"
+        log_dir.mkdir(parents=True, exist_ok=True)
+        log_file = log_dir / log_file
+
+    try:
+        # File handler
+        file_handler = logging.FileHandler(log_file)
+        file_handler.setFormatter(
+            logging.Formatter("%(asctime)s - %(levelname)s - %(message)s")
+        )
+        logger.addHandler(file_handler)
+
+        # Console handler for development
+        if os.environ.get("DEBUG", "false").lower() == "true":
+            console_handler = logging.StreamHandler()
+            console_handler.setFormatter(
+                logging.Formatter("%(levelname)s - %(message)s")
+            )
+            logger.addHandler(console_handler)
+
+        logger.info(f"Logging initialized - file: {log_file}")
+
+    except Exception as e:
+        # Fallback to console only
+        console_handler = logging.StreamHandler()
+        logger.addHandler(console_handler)
+        logger.warning(f"Could not create log file, using console: {e}")
+
+    return logger
+
+
+# Initialize logger
+logger = setup_logging()
+
+# Initialize Langfuse (simplified)
+langfuse = None
+if ENABLE_LANGFUSE:
+    try:
+        langfuse = Langfuse(
+            public_key=os.environ.get("LANGFUSE_PUBLIC_KEY"),
+            secret_key=os.environ.get("LANGFUSE_SECRET_KEY"),
+            host=os.environ.get("LANGFUSE_HOST", "https://cloud.langfuse.com"),
+        )
+        logger.info("Langfuse initialized")
+    except Exception as e:
+        logger.error(f"Langfuse initialization failed: {e}")
+
+# Export observe decorator
+observe = observe if langfuse else lambda *args, **kwargs: lambda func: func