Database Config¶

def get_database_path(self, database_name: str) -> Path:
    """
    Get database file path.

    Parameters
    ----------
    database_name : str
        Database name ('biorempp', 'kegg', 'hadeg', 'toxcsm')

    Returns
    -------
    Path
        Path to database file

    Raises
    ------
    ValueError
        If database name is unknown
    """
    if database_name not in self._config:
        available = list(self._config.keys())
        raise ValueError(
            f"Unknown database: '{database_name}'. " f"Available: {available}"
        )

    filepath = self._config[database_name]["filepath"]
    return Path(filepath)

def get_database_encoding(self, database_name: str, default: str = "utf-8") -> str:
    """
    Get database file encoding.

    Parameters
    ----------
    database_name : str
        Database name.
    default : str, default='utf-8'
        Default encoding if not specified.

    Returns
    -------
    str
        File encoding.
    """
    if database_name not in self._config:
        return default

    return self._config[database_name].get("encoding", default)

def get_database_separator(self, database_name: str, default: str = ";") -> str:
    """
    Get database CSV separator.

    Parameters
    ----------
    database_name : str
        Database name.
    default : str, default=';'
        Default separator if not specified.

    Returns
    -------
    str
        CSV separator.
    """
    if database_name not in self._config:
        return default

    return self._config[database_name].get("separator", default)

def get_all_database_paths(self) -> Dict[str, Path]:
    """
    Get all database paths.

    Returns
    -------
    Dict[str, Path]
        Dictionary mapping database names to paths
    """
    return {name: Path(cfg["filepath"]) for name, cfg in self._config.items()}

def validate_paths(self) -> Dict[str, bool]:
    """
    Validate that all database files exist.

    Returns
    -------
    Dict[str, bool]
        Dictionary mapping database names to existence status
    """
    status = {}

    for name, path in self.get_all_database_paths().items():
        exists = path.exists()
        status[name] = exists

        if not exists:
            logger.warning(f"Database file not found: {name} ({path})")

    return status

def get_database_info(self, database_name: str) -> Dict[str, str]:
    """
    Get complete database configuration.

    Parameters
    ----------
    database_name : str
        Database name.

    Returns
    -------
    Dict[str, str]
        Database configuration dictionary.

    Raises
    ------
    ValueError
        If database name is unknown.
    """
    if database_name not in self._config:
        available = list(self._config.keys())
        raise ValueError(
            f"Unknown database: '{database_name}'. " f"Available: {available}"
        )

    return self._config[database_name].copy()

def get_available_databases(self) -> list[str]:
    """
    Get list of available database names.

    Returns
    -------
    list[str]
        List of database names.
    """
    return list(self._config.keys())