Restructured src to more logical heirachy
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"""
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SQLite database connection management for NHS High-Cost Drug Patient Pathway Analysis Tool.
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Provides connection management, schema initialization, and common database operations.
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Uses context manager pattern for safe resource handling.
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"""
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import sqlite3
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from contextlib import contextmanager
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from pathlib import Path
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from typing import Optional, Generator, Literal
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from core.logging_config import get_logger
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logger = get_logger(__name__)
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class DatabaseConfig:
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"""
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Configuration for SQLite database location and connection parameters.
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Attributes:
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db_path: Path to the SQLite database file
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timeout: Connection timeout in seconds (default: 30)
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isolation_level: Transaction isolation level (default: None for autocommit)
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"""
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DEFAULT_DB_NAME = "pathways.db"
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def __init__(
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self,
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db_path: Optional[Path] = None,
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data_dir: Optional[Path] = None,
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timeout: float = 30.0,
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isolation_level: Optional[Literal['DEFERRED', 'EXCLUSIVE', 'IMMEDIATE']] = None
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):
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"""
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Initialize database configuration.
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Args:
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db_path: Full path to database file. If None, uses data_dir/DEFAULT_DB_NAME.
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data_dir: Directory to place database in. Defaults to ./data/
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timeout: Connection timeout in seconds.
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isolation_level: Transaction isolation level. None = autocommit.
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"""
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if db_path is not None:
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self.db_path = Path(db_path)
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elif data_dir is not None:
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self.db_path = Path(data_dir) / self.DEFAULT_DB_NAME
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else:
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self.db_path = Path("./data") / self.DEFAULT_DB_NAME
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self.timeout = timeout
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self.isolation_level = isolation_level
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def validate(self) -> list[str]:
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"""
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Validate database configuration.
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Returns:
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List of error messages. Empty list means configuration is valid.
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"""
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errors = []
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# Check parent directory exists
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parent_dir = self.db_path.parent
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if not parent_dir.exists():
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errors.append(f"Database directory does not exist: {parent_dir}")
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return errors
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class DatabaseManager:
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"""
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Manages SQLite database connections and operations.
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Provides context manager for safe connection handling and methods
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for common database operations.
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Usage:
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db_manager = DatabaseManager()
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# Using context manager (recommended)
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with db_manager.get_connection() as conn:
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cursor = conn.execute("SELECT * FROM ref_drug_names")
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results = cursor.fetchall()
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# Or get a managed connection for longer operations
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conn = db_manager.connect()
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try:
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# ... do work ...
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finally:
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conn.close()
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"""
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def __init__(self, config: Optional[DatabaseConfig] = None):
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"""
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Initialize the database manager.
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Args:
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config: Database configuration. If None, uses default configuration.
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"""
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self.config = config or DatabaseConfig()
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self._connection: Optional[sqlite3.Connection] = None
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@property
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def db_path(self) -> Path:
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"""Path to the SQLite database file."""
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return self.config.db_path
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@property
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def exists(self) -> bool:
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"""Check if the database file exists."""
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return self.db_path.exists()
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def connect(self) -> sqlite3.Connection:
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"""
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Create a new database connection.
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Returns:
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sqlite3.Connection: New database connection.
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Note:
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The caller is responsible for closing the connection.
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Consider using get_connection() context manager instead.
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"""
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conn = sqlite3.connect(
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str(self.db_path),
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timeout=self.config.timeout,
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isolation_level=self.config.isolation_level
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)
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# Enable foreign key support
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conn.execute("PRAGMA foreign_keys = ON")
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# Return rows as sqlite3.Row for dict-like access
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conn.row_factory = sqlite3.Row
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return conn
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@contextmanager
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def get_connection(self) -> Generator[sqlite3.Connection, None, None]:
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"""
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Context manager for database connections.
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Yields:
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sqlite3.Connection: Database connection.
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Example:
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with db_manager.get_connection() as conn:
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conn.execute("INSERT INTO table VALUES (?)", (value,))
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conn.commit()
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"""
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conn = self.connect()
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try:
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yield conn
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except Exception:
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conn.rollback()
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raise
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finally:
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conn.close()
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@contextmanager
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def get_transaction(self) -> Generator[sqlite3.Connection, None, None]:
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"""
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Context manager for transactional operations.
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Automatically commits on success, rolls back on exception.
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Yields:
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sqlite3.Connection: Database connection in transaction mode.
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Example:
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with db_manager.get_transaction() as conn:
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conn.execute("INSERT INTO table VALUES (?)", (value1,))
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conn.execute("INSERT INTO other_table VALUES (?)", (value2,))
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# Auto-commits if no exception
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"""
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conn = sqlite3.connect(
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str(self.db_path),
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timeout=self.config.timeout,
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isolation_level="DEFERRED" # Explicit transaction mode
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)
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conn.execute("PRAGMA foreign_keys = ON")
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conn.row_factory = sqlite3.Row
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try:
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yield conn
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conn.commit()
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except Exception:
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conn.rollback()
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raise
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finally:
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conn.close()
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def execute_script(self, sql_script: str) -> None:
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"""
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Execute a SQL script (multiple statements).
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Args:
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sql_script: SQL script containing one or more statements.
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"""
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with self.get_connection() as conn:
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conn.executescript(sql_script)
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logger.info("Executed SQL script successfully")
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def table_exists(self, table_name: str) -> bool:
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"""
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Check if a table exists in the database.
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Args:
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table_name: Name of the table to check.
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Returns:
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True if the table exists, False otherwise.
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"""
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with self.get_connection() as conn:
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cursor = conn.execute(
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"SELECT name FROM sqlite_master WHERE type='table' AND name=?",
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(table_name,)
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)
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return cursor.fetchone() is not None
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def get_table_count(self, table_name: str) -> int:
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"""
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Get the row count for a table.
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Args:
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table_name: Name of the table.
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Returns:
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Number of rows in the table.
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"""
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with self.get_connection() as conn:
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# Use parameterized table name via string formatting (safe since we control table_name)
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cursor = conn.execute(f"SELECT COUNT(*) FROM {table_name}")
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result = cursor.fetchone()
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return result[0] if result else 0
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# Default instance for application-wide use
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default_db_config = DatabaseConfig()
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default_db_manager = DatabaseManager(default_db_config)
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