src.core.configurator package

Submodules

src.core.configurator.argument_parser module

This module provides command-line argument parsing functionality for a sequencing data processing script.

It defines:
  • IArgumentParser:

    An interface (via Protocol) specifying a parse() method that returns parsed arguments.

  • ArgumentParser:

    Implements IArgumentParser using Python’s argparse module to define and parse command-line arguments.

Main features:

  • Supports arguments for log file, output directory,

report language, number of threads, and flags for demultiplexor and table manager. - Provides a clear and extendable way to handle command-line inputs for the script.

Usage:

Create an instance of ArgumentParser and call its parse() method to get an argparse.Namespace object with all parsed arguments.

class src.core.configurator.argument_parser.IArgumentParser(*args, **kwargs)[source]

Bases: Protocol

Interface for argument parser classes. Defines a method parse() that returns parsed command-line arguments.

static parse() → Namespace[source]

Parses command-line arguments and returns a Namespace object containing the arguments.

_abc_impl = <_abc._abc_data object>
_is_protocol = True
class src.core.configurator.argument_parser.ArgumentParser(*args, **kwargs)[source]

Bases: IArgumentParser

Implements argument parsing using argparse for sequencing data processing.

Defines command-line arguments such as log file, output directory, report language, etc.

static parse() → Namespace[source]

Set a list of command line arguments and return a compiled object stored these arguments attributes.

_abc_impl = <_abc._abc_data object>
_is_protocol = False

src.core.configurator.config_loader module

This module provides functionality to load configuration settings from a file.

It defines:
  • IConfigLoader:

    An interface (via Protocol) that specifies a load() method for loading configuration data.

  • ConfigLoader:

    Implements IConfigLoader and LoggerMixin to load configuration from an INI file.

Main features:

  • Loads configuration from a specified file path,

defaulting to ‘src/conf/config.ini’. - Reads a specific section (default ‘Pathes’) from the configuration file. - Returns a dictionary containing configuration key-value pairs. - Raises FileNotFoundError if the configuration file does not exist. - Raises ConfigurationError if the section is missing or invalid.

Usage:

Instantiate ConfigLoader, optionally passing a logger, and call load() with the desired file path and section.

class src.core.configurator.config_loader.IConfigLoader(*args, **kwargs)[source]

Bases: Protocol

Interface for configuration loader classes. Defines a load() method to load configuration data.

load() → dict[source]

Loads configuration from a file.

Returns:

A dictionary containing the loaded configuration. Returns an empty dictionary if the file doesn’t exist or is invalid.

Raises:

FileNotFoundError – if loading fails.

_abc_impl = <_abc._abc_data object>
_is_protocol = True
class src.core.configurator.config_loader.ConfigLoader(logger: Logger | None = None)[source]

Bases: LoggerMixin, IConfigLoader

Loads configuration data from an INI file, with logging support.

load(base_config_filepath: PathLike | None = '/home/docs/checkouts/readthedocs.org/user_builds/ngs-analyzer/checkouts/latest/docs/source/src/conf/config.ini', target_section: AnyStr = 'Pathes') → dict[source]

Loads configuration from the specified INI file and section.

Parameters:

  • base_config_filepath (PathLike) – Path to the configuration file.

  • target_section (str) – Section in the configuration file to load.

Returns:

Dictionary with configuration entries from the section.

Return type:

dict

Raises:
_abc_impl = <_abc._abc_data object>
_is_protocol = False

src.core.configurator.configuration_error module

This module provides the base ConfigurationError exception for the project.

exception src.core.configurator.configuration_error.ConfigurationError[source]

Bases: Exception

Exception raised for errors related to configuration issues.

message

Human-readable string describing the error.

Type:

str

src.core.configurator.logging_configurator module

This module provides functions for validating and potentially creating file and directory paths. It aims to ensure consistent path handling throughout a larger system, preventing errors related to missing or incorrectly specified paths. The module leverages the IPathValidator interface for flexibility and maintainability.

Functions:
  • validate_path:

    Validates a path and optionally creates it if it doesn’t exist.

Classes:
  • FileValidator:

    Validates file paths, checking for existence and potentially raising exceptions.

  • DirectoryValidator:

    Validates directory paths, checking for existence and potentially creating directories.

  • IPathValidator:

    Abstract base class defining the contract for path validation.

class src.core.configurator.logging_configurator.ILoggingConfigurator(*args, **kwargs)[source]

Bases: Protocol

Protocol for configuring logging. Implementations should provide a method to set a logger instance.

set_logger(silent: bool = False) → Logger[source]

Configures and returns a logger instance.

Parameters:

silent (bool, optional) – If True, suppresses output to console. Defaults to False.

Returns:

Configured logger instance.

Return type:

logging.Logger

_abc_impl = <_abc._abc_data object>
_is_protocol = True
class src.core.configurator.logging_configurator.LoggingConfigurator(path_validator: IPathValidator, log_path: PathLike = '.', args: Namespace = None)[source]

Bases: ILoggingConfigurator

Configures logging to a specified file or console.

_abc_impl = <_abc._abc_data object>
_is_protocol = False
set_logger(silent: bool = False) → Logger[source]

Sets up logging configuration, creating log files and handlers.

Parameters:

silent (bool) – If True, disables console output. Defaults to False.

Returns:

Configured logger instance.

Return type:

logging.Logger

Raises:

SystemExit – If verification or creation of log path fails.

src.core.configurator.path_validator module

This module defines an interface for validating file paths.

The IPathValidator protocol outlines the method for verifying the existence of a given path.

It’s designed to be used by classes that need to ensure the validity of file paths before proceeding with operations.

The module also imports necessary modules, including logging for logging, os for path manipulation, and typing for type hinting.

Crucially, it imports touch from src.core.base which provides a function to create a file or directory if it doesn’t exist.

class src.core.configurator.path_validator.IPathValidator(*args, **kwargs)[source]

Bases: Protocol

Interface for validating file or directory paths.

This abstract class defines the contract for classes responsible for verifying the existence and potentially creating paths.

Subclasses must implement the verify_path method.

This class is intended to be used in a larger system to enforce consistent path handling and validation.

verify_path(src: PathLike, create_if_missing: bool = False) → bool[source]

Verifies the existence of the specified path.

Parameters:

  • src (PathLike[AnyStr]) – The file or directory path to verify.

  • create_if_missing (bool, optional) – If True, creates the path if it does not exist. Defaults to False.

Returns:

True if the path exists or was successfully created; otherwise, False.

Return type:

bool

_abc_impl = <_abc._abc_data object>
_is_protocol = True
class src.core.configurator.path_validator.PathValidator(logger: Logger = None)[source]

Bases: LoggerMixin, IPathValidator

Validates the existence of a file, optionally creating it if missing.

verify_path(src: PathLike, create_if_missing: bool = False) → bool[source]

Checks the existence of the file or directory at the given path src.

If the path does not exist, creates the necessary directories and the file.

Parameters:

  • src (PathLike[AnyStr]) – The path to the file or directory to check or create.

  • create_if_missing (bool) – Whether to create the path if it doesn’t exist. Defaults to False.

Returns:

True if the path exists or was successfully created, otherwise False.

Return type:

bool

_abc_impl = <_abc._abc_data object>
_is_protocol = False

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