medcat.utils.defaults

Classes:

• LegacyConversionDisabledError –

  Raised when legacy conversion is disabled.

• StatusTypes –

Functions:

• avoid_legacy_conversion –
• default_weighted_average –
• doing_legacy_conversion_message –
• workers –

  Get number of workers.

Attributes:

• AVOID_LEGACY_CONVERSION_ENVIRON –
• COMPONENTS_FOLDER –
• DEFAULT_MINOR_FOR_INFO –
• DEFAULT_PACK_NAME –
• DEFAULT_PATCH_FOR_INFO –
• DEFAULT_PYPI_URL –
• DEFAULT_SPACY_MODEL –
• DEFAULT_VERSION_INFO_LEVEL –
• DEFAULT_VERSION_INFO_YANKED_LEVEL –
• MEDCAT_DISABLE_VERSION_CHECK_ENVIRON –
• MEDCAT_MINOR_UPDATE_THRESHOLD_ENVIRON –
• MEDCAT_PATCH_UPDATE_THRESHOLD_ENVIRON –
• MEDCAT_PYPI_URL_ENVIRON –
• MEDCAT_VERSION_UPDATE_LOG_LEVEL_ENVIRON –
• MEDCAT_VERSION_UPDATE_YANKED_LOG_LEVEL_ENVIRON –

AVOID_LEGACY_CONVERSION_ENVIRON module-attribute

AVOID_LEGACY_CONVERSION_ENVIRON = 'MEDCAT_AVOID_LECACY_CONVERSION'

COMPONENTS_FOLDER module-attribute

COMPONENTS_FOLDER = 'saved_components'

DEFAULT_MINOR_FOR_INFO module-attribute

DEFAULT_MINOR_FOR_INFO = 3

DEFAULT_PACK_NAME module-attribute

DEFAULT_PACK_NAME = 'medcat2_model_pack'

DEFAULT_PATCH_FOR_INFO module-attribute

DEFAULT_PATCH_FOR_INFO = 3

DEFAULT_PYPI_URL module-attribute

DEFAULT_PYPI_URL = 'https://pypi.org/pypi'

DEFAULT_SPACY_MODEL module-attribute

DEFAULT_SPACY_MODEL = 'en_core_web_md'

DEFAULT_VERSION_INFO_LEVEL module-attribute

DEFAULT_VERSION_INFO_LEVEL = 'INFO'

DEFAULT_VERSION_INFO_YANKED_LEVEL module-attribute

DEFAULT_VERSION_INFO_YANKED_LEVEL = 'WARNING'

MEDCAT_DISABLE_VERSION_CHECK_ENVIRON module-attribute

MEDCAT_DISABLE_VERSION_CHECK_ENVIRON = 'MEDCAT_DISABLE_VERSION_CHECK'

MEDCAT_MINOR_UPDATE_THRESHOLD_ENVIRON module-attribute

MEDCAT_MINOR_UPDATE_THRESHOLD_ENVIRON = 'MEDCAT_MINOR_UPDATE_THRESHOLD'

MEDCAT_PATCH_UPDATE_THRESHOLD_ENVIRON module-attribute

MEDCAT_PATCH_UPDATE_THRESHOLD_ENVIRON = 'MEDCAT_PATCH_UPDATE_THRESHOLD'

MEDCAT_PYPI_URL_ENVIRON module-attribute

MEDCAT_PYPI_URL_ENVIRON = 'MEDCAT_PYPI_URL'

MEDCAT_VERSION_UPDATE_LOG_LEVEL_ENVIRON module-attribute

MEDCAT_VERSION_UPDATE_LOG_LEVEL_ENVIRON = 'MEDCAT_VERSION_UPDATE_LOG_LEVEL'

MEDCAT_VERSION_UPDATE_YANKED_LOG_LEVEL_ENVIRON module-attribute

MEDCAT_VERSION_UPDATE_YANKED_LOG_LEVEL_ENVIRON = 'MEDCAT_VERSION_UPDATE_YANKED_LOG_LEVEL'

LegacyConversionDisabledError

LegacyConversionDisabledError(component_name: str)

Bases: Exception

Raised when legacy conversion is disabled.

Source code in medcat-v2/medcat/utils/defaults.py

def __init__(self, component_name: str):
    super().__init__(
        f"Legacy conversion is disabled (while loading {component_name}). "
        f"Set the environment variable {AVOID_LEGACY_CONVERSION_ENVIRON} "
        "to `False` to allow conversion.")

StatusTypes

Attributes:

• ALLOWED_STATUS –
• AUTOMATIC –
• DO_DISAMBUGATION –
• MUST_DISAMBIGATE –
• PRIMARY_STATUS (set[str]) –
• PRIMARY_STATUS_NO_DISAMB –
• PRIMARY_STATUS_W_DISAMB –

ALLOWED_STATUS class-attribute instance-attribute

ALLOWED_STATUS = {PRIMARY_STATUS_NO_DISAMB, MUST_DISAMBIGATE, AUTOMATIC}

AUTOMATIC class-attribute instance-attribute

AUTOMATIC = 'A'

DO_DISAMBUGATION class-attribute instance-attribute

DO_DISAMBUGATION = {MUST_DISAMBIGATE, PRIMARY_STATUS_W_DISAMB}

MUST_DISAMBIGATE class-attribute instance-attribute

MUST_DISAMBIGATE = 'N'

PRIMARY_STATUS class-attribute instance-attribute

PRIMARY_STATUS: set[str] = {PRIMARY_STATUS_NO_DISAMB, PRIMARY_STATUS_W_DISAMB}

PRIMARY_STATUS_NO_DISAMB class-attribute instance-attribute

PRIMARY_STATUS_NO_DISAMB = 'P'

PRIMARY_STATUS_W_DISAMB class-attribute instance-attribute

PRIMARY_STATUS_W_DISAMB = 'PD'

avoid_legacy_conversion

avoid_legacy_conversion() -> bool

Source code in medcat-v2/medcat/utils/defaults.py

def avoid_legacy_conversion() -> bool:
    return os.environ.get(
        AVOID_LEGACY_CONVERSION_ENVIRON, "False").lower() == "true"

default_weighted_average cached

default_weighted_average(step: int, factor: float = 0.0004) -> float

Source code in medcat-v2/medcat/utils/defaults.py

@lru_cache(maxsize=100)
def default_weighted_average(step: int, factor: float = 0.0004) -> float:
    return max(0.1, 1 - (step ** 2 * factor))

doing_legacy_conversion_message

doing_legacy_conversion_message(logger: Logger, component_name: str, file_path: str = '', level: int = WARNING) -> None

Source code in medcat-v2/medcat/utils/defaults.py

def doing_legacy_conversion_message(
        logger: logging.Logger, component_name: str, file_path: str = '',
        level: int = logging.WARNING
        ) -> None:
    logger.log(
        level,
        "Doing legacy conversion on %s (at '%s'). "
        "Set the environment variable %s "
        "to `True` to avoid this.",
        component_name, file_path, AVOID_LEGACY_CONVERSION_ENVIRON)

workers

workers(workers_override: Optional[int] = None) -> int

Get number of workers.

Either the number of workers specified (if done so). Or the number of workers available (i.e cpu count - 1).

Parameters:

• workers_override

  (Optional[int], default: None ) –

  The number of workers to use. Defaults to None.

Returns:

• int ( int ) –

  description

Source code in medcat-v2/medcat/utils/defaults.py

def workers(workers_override: Optional[int] = None) -> int:
    """Get number of workers.

    Either the number of workers specified (if done so).
    Or the number of workers available (i.e cpu count - 1).

    Args:
        workers_override (Optional[int], optional):
            The number of workers to use. Defaults to None.

    Returns:
        int: _description_
    """
    if workers_override is not None:
        return workers_override
    return max(cpu_count() - 1, 1)