Authentication

BioEPICAuth

BioEPICAuth

Bases: APIBase

Authentication handler for BioEPIC API operations.

You must provide either: - client_id and client_secret (for client credentials grant), OR - username and password (for password grant).

Parameters:

Name	Type	Description	Default
client_id	str	The client ID for BioEPIC API authentication (required if using client credentials grant).	None
client_secret	str	The client secret for BioEPIC API authentication (required if using client credentials grant).	None
username	str	The username for BioEPIC API authentication (required if using password grant).	None
password	str	The password for BioEPIC API authentication (required if using password grant).	None

Notes

Security Warning: Your client_id and client_secret should be stored in a secure location. We recommend using environment variables. Do not hard code these values in your code.

Source code in bioepic_skills/auth.py

class BioEPICAuth(APIBase):
    """
    Authentication handler for BioEPIC API operations.

    You must provide either:
      - client_id and client_secret (for client credentials grant), OR
      - username and password (for password grant).

    Parameters
    ----------
    client_id : str
        The client ID for BioEPIC API authentication (required if using client credentials grant).
    client_secret : str
        The client secret for BioEPIC API authentication (required if using client credentials grant).
    username : str
        The username for BioEPIC API authentication (required if using password grant).
    password : str
        The password for BioEPIC API authentication (required if using password grant).

    Notes
    -----
    Security Warning: Your client_id and client_secret should be stored in a secure location.
        We recommend using environment variables.
        Do not hard code these values in your code.
    """

    def __init__(
        self,
        client_id: str | None = None,
        client_secret: str | None = None,
        username: str | None = None,
        password: str | None = None,
        env: str = "prod",
    ):
        super().__init__(env=env)
        self.client_id = client_id
        self.client_secret = client_secret
        self.username = username
        self.password = password
        self.token = None
        self.token_expiry = None

    def has_credentials(self) -> bool:
        """Check if the credentials are passed in properly."""
        has_client_creds = self.client_id is not None and self.client_secret is not None
        has_user_creds = self.username is not None and self.password is not None
        return has_client_creds or has_user_creds

    def get_token(self) -> str:
        """Get a valid access token, refreshing if necessary."""
        if self.token and self._is_token_valid():
            return self.token
        return self._refresh_token()

    def _is_token_valid(self) -> bool:
        """Check if current token is valid and not expired."""
        if not self.token or not self.token_expiry:
            return False
        # Add a 5-minute buffer before expiry
        return datetime.now() < (self.token_expiry - timedelta(minutes=5))

    def _refresh_token(self) -> str:
        """Refresh the access token."""
        url = f"{self.base_url}/token"

        if self.client_id and self.client_secret:
            # Client credentials grant
            data = {
                "grant_type": "client_credentials",
                "client_id": self.client_id,
                "client_secret": self.client_secret,
            }
        elif self.username and self.password:
            # Password grant
            data = {
                "grant_type": "password",
                "username": self.username,
                "password": self.password,
            }
        else:
            raise ValueError("No valid credentials provided")

        try:
            response = requests.post(url, data=data)
            response.raise_for_status()
            token_data = response.json()
            self.token = token_data["access_token"]
            # Assuming token includes expires_in field in seconds
            expires_in = token_data.get("expires_in", 3600)
            self.token_expiry = datetime.now() + timedelta(seconds=expires_in)
            logging.debug("Token refreshed successfully")
            return self.token
        except requests.exceptions.RequestException as e:
            logger.error("Failed to refresh token", exc_info=True)
            raise RuntimeError("Failed to authenticate with BioEPIC API") from e

has_credentials

has_credentials() -> bool

Check if the credentials are passed in properly.

Source code in bioepic_skills/auth.py

def has_credentials(self) -> bool:
    """Check if the credentials are passed in properly."""
    has_client_creds = self.client_id is not None and self.client_secret is not None
    has_user_creds = self.username is not None and self.password is not None
    return has_client_creds or has_user_creds

get_token

get_token() -> str

Get a valid access token, refreshing if necessary.

Source code in bioepic_skills/auth.py

def get_token(self) -> str:
    """Get a valid access token, refreshing if necessary."""
    if self.token and self._is_token_valid():
        return self.token
    return self._refresh_token()

Decorators

requires_auth

requires_auth

requires_auth(f)

Decorator for methods that need authentication

Source code in bioepic_skills/decorators.py

def requires_auth(f):
    """Decorator for methods that need authentication"""

    @wraps(f)
    def wrapper(self, *args, **kwargs):
        # Get function parameter names (excluding 'self')
        import inspect

        sig = inspect.signature(f)
        param_names = list(sig.parameters.keys())[1:]  # Skip 'self'

        # Create a dictionary of all arguments (positional + keyword)
        bound_args = {}
        for i, arg in enumerate(args):
            if i < len(param_names):
                bound_args[param_names[i]] = arg
        bound_args.update(kwargs)

        # Check if client_id and client_secret are provided
        client_id = bound_args.get("client_id")
        client_secret = bound_args.get("client_secret")

        # If credentials provided in function call, proceed
        if client_id is not None and client_secret is not None:
            return f(self, *args, **kwargs)

        if not self.auth.has_credentials():
            raise AuthenticationError(
                f"{f.__name__} requires authentication. Either provide `client_id` and `client_secret` OR `username` and `password`."
            )
        return f(self, *args, **kwargs)

    return wrapper

AuthenticationError

AuthenticationError

Bases: Exception

Custom exception for authentication failures.

Source code in bioepic_skills/decorators.py

class AuthenticationError(Exception):
    """Custom exception for authentication failures."""
    pass