Andrew Charlwood
76838887e6
Move 6 packages (core, config, data_processing, analysis, visualization, cli) into src/ to reduce root clutter. Merge tools/data.py into data_processing/transforms.py. Move docs to docs/. Path resolution via .pth file (setup_dev.py), pytest pythonpath config, and sys.path bootstrap in rxconfig.py and CLI entry points. Clean up pyproject.toml deps (remove stale pins, add snowflake-connector-python). Fix tomllib import for Python 3.10 compatibility. All 113 tests pass.
122 lines
3.5 KiB
Python
122 lines
3.5 KiB
Python
"""
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Logging configuration for NHS High-Cost Drug Patient Pathway Analysis Tool.
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Provides structured logging setup with console and optional file handlers.
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"""
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import logging
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import sys
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from datetime import datetime
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from pathlib import Path
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from typing import Optional
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# Default log format: timestamp, level, module name, message
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DEFAULT_FORMAT = "%(asctime)s [%(levelname)s] %(name)s: %(message)s"
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DEFAULT_DATE_FORMAT = "%Y-%m-%d %H:%M:%S"
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# Simplified format for console output (used when redirecting to GUI)
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SIMPLE_FORMAT = "%(message)s"
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def setup_logging(
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level: int = logging.INFO,
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log_dir: Optional[Path] = None,
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console: bool = True,
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file_logging: bool = False,
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simple_console: bool = False,
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) -> logging.Logger:
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"""
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Configure application-wide logging.
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Args:
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level: Logging level (default: INFO)
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log_dir: Directory for log files (default: ./logs/)
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console: Whether to log to console/stdout (default: True)
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file_logging: Whether to log to file (default: False)
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simple_console: Use simplified format for console (just message, no timestamp)
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Returns:
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Root logger configured for the application
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Usage:
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# Basic setup - console only
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logger = setup_logging()
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# With file logging
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logger = setup_logging(file_logging=True)
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# Debug mode
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logger = setup_logging(level=logging.DEBUG)
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# GUI mode - simple format for stdout capture
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logger = setup_logging(simple_console=True)
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"""
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# Get root logger for the application
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root_logger = logging.getLogger("pathways")
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# Clear any existing handlers to avoid duplicates on re-initialization
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root_logger.handlers.clear()
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root_logger.setLevel(level)
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# Console handler
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if console:
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console_handler = logging.StreamHandler(sys.stdout)
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console_handler.setLevel(level)
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if simple_console:
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console_format = logging.Formatter(SIMPLE_FORMAT)
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else:
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console_format = logging.Formatter(DEFAULT_FORMAT, datefmt=DEFAULT_DATE_FORMAT)
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console_handler.setFormatter(console_format)
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root_logger.addHandler(console_handler)
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# File handler
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if file_logging:
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if log_dir is None:
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log_dir = Path("./logs")
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log_dir.mkdir(parents=True, exist_ok=True)
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log_filename = f"pathways_{datetime.now().strftime('%Y%m%d_%H%M%S')}.log"
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log_path = log_dir / log_filename
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file_handler = logging.FileHandler(log_path, encoding="utf-8")
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file_handler.setLevel(level)
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file_handler.setFormatter(
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logging.Formatter(DEFAULT_FORMAT, datefmt=DEFAULT_DATE_FORMAT)
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)
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root_logger.addHandler(file_handler)
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return root_logger
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def get_logger(name: str) -> logging.Logger:
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"""
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Get a logger for a specific module.
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Args:
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name: Module name (typically __name__)
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Returns:
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Logger instance configured as child of root pathways logger
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Usage:
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from core.logging_config import get_logger
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logger = get_logger(__name__)
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logger.info("Processing started")
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logger.error("Something went wrong")
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"""
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# Create child logger under the pathways namespace
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if name.startswith("pathways."):
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return logging.getLogger(name)
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return logging.getLogger(f"pathways.{name}")
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# Module-level loggers for common components
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data_logger = get_logger("data")
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dashboard_logger = get_logger("dashboard")
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gui_logger = get_logger("gui")
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