refactor: reorganize repository to src/ layout
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.
This commit is contained in:
Andrew Charlwood
@@ -1,239 +0,0 @@
|
||||
"""
|
||||
SQLite database connection management for NHS High-Cost Drug Patient Pathway Analysis Tool.
|
||||
|
||||
Provides connection management, schema initialization, and common database operations.
|
||||
Uses context manager pattern for safe resource handling.
|
||||
"""
|
||||
|
||||
import sqlite3
|
||||
from contextlib import contextmanager
|
||||
from pathlib import Path
|
||||
from typing import Optional, Generator, Literal
|
||||
|
||||
from core.logging_config import get_logger
|
||||
|
||||
logger = get_logger(__name__)
|
||||
|
||||
|
||||
class DatabaseConfig:
|
||||
"""
|
||||
Configuration for SQLite database location and connection parameters.
|
||||
|
||||
Attributes:
|
||||
db_path: Path to the SQLite database file
|
||||
timeout: Connection timeout in seconds (default: 30)
|
||||
isolation_level: Transaction isolation level (default: None for autocommit)
|
||||
"""
|
||||
|
||||
DEFAULT_DB_NAME = "pathways.db"
|
||||
|
||||
def __init__(
|
||||
self,
|
||||
db_path: Optional[Path] = None,
|
||||
data_dir: Optional[Path] = None,
|
||||
timeout: float = 30.0,
|
||||
isolation_level: Optional[Literal['DEFERRED', 'EXCLUSIVE', 'IMMEDIATE']] = None
|
||||
):
|
||||
"""
|
||||
Initialize database configuration.
|
||||
|
||||
Args:
|
||||
db_path: Full path to database file. If None, uses data_dir/DEFAULT_DB_NAME.
|
||||
data_dir: Directory to place database in. Defaults to ./data/
|
||||
timeout: Connection timeout in seconds.
|
||||
isolation_level: Transaction isolation level. None = autocommit.
|
||||
"""
|
||||
if db_path is not None:
|
||||
self.db_path = Path(db_path)
|
||||
elif data_dir is not None:
|
||||
self.db_path = Path(data_dir) / self.DEFAULT_DB_NAME
|
||||
else:
|
||||
self.db_path = Path("./data") / self.DEFAULT_DB_NAME
|
||||
|
||||
self.timeout = timeout
|
||||
self.isolation_level = isolation_level
|
||||
|
||||
def validate(self) -> list[str]:
|
||||
"""
|
||||
Validate database configuration.
|
||||
|
||||
Returns:
|
||||
List of error messages. Empty list means configuration is valid.
|
||||
"""
|
||||
errors = []
|
||||
|
||||
# Check parent directory exists
|
||||
parent_dir = self.db_path.parent
|
||||
if not parent_dir.exists():
|
||||
errors.append(f"Database directory does not exist: {parent_dir}")
|
||||
|
||||
return errors
|
||||
|
||||
|
||||
class DatabaseManager:
|
||||
"""
|
||||
Manages SQLite database connections and operations.
|
||||
|
||||
Provides context manager for safe connection handling and methods
|
||||
for common database operations.
|
||||
|
||||
Usage:
|
||||
db_manager = DatabaseManager()
|
||||
|
||||
# Using context manager (recommended)
|
||||
with db_manager.get_connection() as conn:
|
||||
cursor = conn.execute("SELECT * FROM ref_drug_names")
|
||||
results = cursor.fetchall()
|
||||
|
||||
# Or get a managed connection for longer operations
|
||||
conn = db_manager.connect()
|
||||
try:
|
||||
# ... do work ...
|
||||
finally:
|
||||
conn.close()
|
||||
"""
|
||||
|
||||
def __init__(self, config: Optional[DatabaseConfig] = None):
|
||||
"""
|
||||
Initialize the database manager.
|
||||
|
||||
Args:
|
||||
config: Database configuration. If None, uses default configuration.
|
||||
"""
|
||||
self.config = config or DatabaseConfig()
|
||||
self._connection: Optional[sqlite3.Connection] = None
|
||||
|
||||
@property
|
||||
def db_path(self) -> Path:
|
||||
"""Path to the SQLite database file."""
|
||||
return self.config.db_path
|
||||
|
||||
@property
|
||||
def exists(self) -> bool:
|
||||
"""Check if the database file exists."""
|
||||
return self.db_path.exists()
|
||||
|
||||
def connect(self) -> sqlite3.Connection:
|
||||
"""
|
||||
Create a new database connection.
|
||||
|
||||
Returns:
|
||||
sqlite3.Connection: New database connection.
|
||||
|
||||
Note:
|
||||
The caller is responsible for closing the connection.
|
||||
Consider using get_connection() context manager instead.
|
||||
"""
|
||||
conn = sqlite3.connect(
|
||||
str(self.db_path),
|
||||
timeout=self.config.timeout,
|
||||
isolation_level=self.config.isolation_level
|
||||
)
|
||||
# Enable foreign key support
|
||||
conn.execute("PRAGMA foreign_keys = ON")
|
||||
# Return rows as sqlite3.Row for dict-like access
|
||||
conn.row_factory = sqlite3.Row
|
||||
return conn
|
||||
|
||||
@contextmanager
|
||||
def get_connection(self) -> Generator[sqlite3.Connection, None, None]:
|
||||
"""
|
||||
Context manager for database connections.
|
||||
|
||||
Yields:
|
||||
sqlite3.Connection: Database connection.
|
||||
|
||||
Example:
|
||||
with db_manager.get_connection() as conn:
|
||||
conn.execute("INSERT INTO table VALUES (?)", (value,))
|
||||
conn.commit()
|
||||
"""
|
||||
conn = self.connect()
|
||||
try:
|
||||
yield conn
|
||||
except Exception:
|
||||
conn.rollback()
|
||||
raise
|
||||
finally:
|
||||
conn.close()
|
||||
|
||||
@contextmanager
|
||||
def get_transaction(self) -> Generator[sqlite3.Connection, None, None]:
|
||||
"""
|
||||
Context manager for transactional operations.
|
||||
|
||||
Automatically commits on success, rolls back on exception.
|
||||
|
||||
Yields:
|
||||
sqlite3.Connection: Database connection in transaction mode.
|
||||
|
||||
Example:
|
||||
with db_manager.get_transaction() as conn:
|
||||
conn.execute("INSERT INTO table VALUES (?)", (value1,))
|
||||
conn.execute("INSERT INTO other_table VALUES (?)", (value2,))
|
||||
# Auto-commits if no exception
|
||||
"""
|
||||
conn = sqlite3.connect(
|
||||
str(self.db_path),
|
||||
timeout=self.config.timeout,
|
||||
isolation_level="DEFERRED" # Explicit transaction mode
|
||||
)
|
||||
conn.execute("PRAGMA foreign_keys = ON")
|
||||
conn.row_factory = sqlite3.Row
|
||||
try:
|
||||
yield conn
|
||||
conn.commit()
|
||||
except Exception:
|
||||
conn.rollback()
|
||||
raise
|
||||
finally:
|
||||
conn.close()
|
||||
|
||||
def execute_script(self, sql_script: str) -> None:
|
||||
"""
|
||||
Execute a SQL script (multiple statements).
|
||||
|
||||
Args:
|
||||
sql_script: SQL script containing one or more statements.
|
||||
"""
|
||||
with self.get_connection() as conn:
|
||||
conn.executescript(sql_script)
|
||||
logger.info("Executed SQL script successfully")
|
||||
|
||||
def table_exists(self, table_name: str) -> bool:
|
||||
"""
|
||||
Check if a table exists in the database.
|
||||
|
||||
Args:
|
||||
table_name: Name of the table to check.
|
||||
|
||||
Returns:
|
||||
True if the table exists, False otherwise.
|
||||
"""
|
||||
with self.get_connection() as conn:
|
||||
cursor = conn.execute(
|
||||
"SELECT name FROM sqlite_master WHERE type='table' AND name=?",
|
||||
(table_name,)
|
||||
)
|
||||
return cursor.fetchone() is not None
|
||||
|
||||
def get_table_count(self, table_name: str) -> int:
|
||||
"""
|
||||
Get the row count for a table.
|
||||
|
||||
Args:
|
||||
table_name: Name of the table.
|
||||
|
||||
Returns:
|
||||
Number of rows in the table.
|
||||
"""
|
||||
with self.get_connection() as conn:
|
||||
# Use parameterized table name via string formatting (safe since we control table_name)
|
||||
cursor = conn.execute(f"SELECT COUNT(*) FROM {table_name}")
|
||||
result = cursor.fetchone()
|
||||
return result[0] if result else 0
|
||||
|
||||
|
||||
# Default instance for application-wide use
|
||||
default_db_config = DatabaseConfig()
|
||||
default_db_manager = DatabaseManager(default_db_config)
|
||||
Reference in New Issue
Block a user