Configuration Manager API

Configuration Management System for VarAnnote v1.0.0

Provides comprehensive configuration management including: - YAML configuration file loading - Environment variable overrides - User preference management - Configuration validation - Default value handling

class varannote.utils.config_manager.DatabaseConfig(name, priority=5, api_key=None, rate_limit=5.0, timeout=30, enabled=True)

Bases: object

Database configuration settings

name: str

priority: int = 5

api_key: Optional[str] = None

rate_limit: float = 5.0

timeout: int = 30

enabled: bool = True

__init__(name, priority=5, api_key=None, rate_limit=5.0, timeout=30, enabled=True)

class varannote.utils.config_manager.PerformanceConfig(max_workers=4, use_parallel=True, batch_size=50, max_concurrent_requests=30, max_cache_size_mb=500, cache_cleanup_interval=3600, max_connections=100, max_connections_per_host=30)

Bases: object

Performance configuration settings

max_workers: int = 4

use_parallel: bool = True

batch_size: int = 50

max_concurrent_requests: int = 30

max_cache_size_mb: int = 500

cache_cleanup_interval: int = 3600

max_connections: int = 100

max_connections_per_host: int = 30

__init__(max_workers=4, use_parallel=True, batch_size=50, max_concurrent_requests=30, max_cache_size_mb=500, cache_cleanup_interval=3600, max_connections=100, max_connections_per_host=30)

class varannote.utils.config_manager.CacheConfig(enabled=True, directory='~/.varannote/cache', max_age_days=30, max_size_gb=2.0, compression=True, strategies=None)

Bases: object

Cache configuration settings

enabled: bool = True

directory: str = '~/.varannote/cache'

max_age_days: int = 30

max_size_gb: float = 2.0

compression: bool = True

strategies: Dict[str, str] = None

__init__(enabled=True, directory='~/.varannote/cache', max_age_days=30, max_size_gb=2.0, compression=True, strategies=None)

class varannote.utils.config_manager.OutputConfig(default_format='vcf', available_formats=None, include_fields=None, filters=None)

Bases: object

Output configuration settings

default_format: str = 'vcf'

available_formats: List[str] = None

include_fields: List[str] = None

filters: Dict[str, Any] = None

__init__(default_format='vcf', available_formats=None, include_fields=None, filters=None)

class varannote.utils.config_manager.LoggingConfig(level='INFO', directory='~/.varannote/logs', max_file_size_mb=10, backup_count=5, categories=None)

Bases: object

Logging configuration settings

level: str = 'INFO'

directory: str = '~/.varannote/logs'

max_file_size_mb: int = 10

backup_count: int = 5

categories: Dict[str, bool] = None

__init__(level='INFO', directory='~/.varannote/logs', max_file_size_mb=10, backup_count=5, categories=None)

class varannote.utils.config_manager.ConfigManager(config_file=None, user_config_dir=None)

Bases: object

Comprehensive configuration manager for VarAnnote

Features: - YAML configuration file loading - Environment variable overrides - Configuration validation - Default value management - User preference handling - Configuration merging and inheritance

__init__(config_file=None, user_config_dir=None)

Initialize configuration manager

Parameters:

• config_file (Union[str, Path, None]) – Path to main configuration file

• user_config_dir (Union[str, Path, None]) – Directory for user-specific configurations

get(key, default=None)

Get configuration value by key

Return type:

Any

set(key, value)

Set configuration value by key

get_database_config(database_name)

Get database configuration

Return type:

Optional[DatabaseConfig]

get_enabled_databases()

Get list of enabled databases sorted by priority

Return type:

List[str]

save_user_config(config_updates)

Save user configuration updates

export_config(output_file, format='yaml')

Export current configuration to file

get_config_summary()

Get configuration summary

Return type:

Dict[str, Any]

varannote.utils.config_manager.get_config_manager(**kwargs)

Get global configuration manager instance

Return type:

ConfigManager

varannote.utils.config_manager.get_config(key, default=None)

Get configuration value

Return type:

Any

varannote.utils.config_manager.get_database_config(database_name)

Get database configuration

Return type:

Optional[DatabaseConfig]

varannote.utils.config_manager.get_enabled_databases()

Get enabled databases sorted by priority

Return type:

List[str]