config

autocorpus.config

Contains a loader for default configuration files.

Classes

DefaultConfig(filename)

Bases: Enum

An enumeration representing different configuration files for various datasets.

Attributes:

Name	Type	Description
LEGACY_PMC		Configuration file for legacy PMC data (pre-October 2024).
PMC		Configuration file for current PMC data.
PLOS_GENETICS		Configuration file for PLOS Genetics data.
NATURE_GENETICS		Configuration file for Nature Genetics data.

Methods:

Name	Description
load_config	Loads and returns the configuration from the associated file. The configuration is lazy-loaded and cached upon first access.

Initializes the DefaultConfig enum with the given filename.

Parameters:

Name	Type	Description	Default
filename	str	The name of the configuration file to load.	required

Source code in autocorpus/config.py

def __init__(self, filename: str) -> None:
    """Initializes the DefaultConfig enum with the given filename.

    Args:
        filename: The name of the configuration file to load.
    """
    self._filename = filename
    self._config: dict[str, Any] = {}  # Lazy-loaded cache

Functions

load_config()

Loads the configuration file when first accessed.

Returns:

Type	Description
dict[str, Any]	The configuration file as a dictionary.

Source code in autocorpus/config.py

def load_config(self) -> dict[str, Any]:
    """Loads the configuration file when first accessed.

    Returns:
        The configuration file as a dictionary.
    """
    if self._config == {}:
        config_path = resources.files("autocorpus.configs") / self._filename
        with config_path.open("r", encoding="utf-8") as f_in:
            self._config = json.load(f_in)["config"]
    return self._config

Functions

read_config(config_path)

Reads a configuration file and returns its contents.

Parameters:

Name	Type	Description	Default
config_path	str	The path to the configuration file.	required

Returns:

Name	Type	Description
dict	dict[str, Any]	The contents of the configuration file.

Raises:

Type	Description
FileNotFoundError	If the configuration file does not exist.
JSONDecodeError	If the configuration file is not a valid JSON.
KeyError	If the configuration file does not contain the expected "config" key.

Source code in autocorpus/config.py

def read_config(config_path: str) -> dict[str, Any]:
    """Reads a configuration file and returns its contents.

    Args:
        config_path: The path to the configuration file.

    Returns:
        dict: The contents of the configuration file.

    Raises:
        FileNotFoundError: If the configuration file does not exist.
        json.JSONDecodeError: If the configuration file is not a valid JSON.
        KeyError: If the configuration file does not contain the expected "config" key.
    """
    with open(config_path, encoding="utf-8") as f:
        ## TODO: validate config file here if possible
        content = json.load(f)
        return content["config"]