fix: Update NBIA toolkit dependencies and fix base URL references.

src/nbiatoolkit/auth.py

@@ -1,7 +1,7 @@
 import requests
 import time
 from typing import Union, Tuple
-from .utils import NBIA_ENDPOINTS
+from .utils import NBIA_ENDPOINTS, NBIA_BASE_URLS
 from cryptography.fernet import Fernet
 
 
@@ -113,7 +113,7 @@ def __init__(
         username: str = "nbia_guest",
         password: str = "",
         client_id: str = "NBIA",
-        base_url: Union[str, NBIA_ENDPOINTS] = NBIA_ENDPOINTS.NBIA,
+        base_url: str | NBIA_BASE_URLS = NBIA_BASE_URLS.NBIA,
     ) -> None:
         """
         Initialize the OAuth2 class.
@@ -127,7 +127,7 @@ def __init__(
             The password for authentication. Default is an empty string.
         client_id : str, optional
             The client ID for authentication. Default is "NBIA".
-        base_url : str or NBIA_ENDPOINTS, optional. Default is NBIA_ENDPOINTS.NBIA
+        base_url : str or NBIA_BASE_URLS, optional. Default is NBIA_BASE_URLS.NBIA
 
         """
 
@@ -143,7 +143,7 @@ def __init__(
             key=self._fernet_key, username=username, password=password
         )
 
-        if isinstance(base_url, NBIA_ENDPOINTS):
+        if isinstance(base_url, NBIA_BASE_URLS):
             self.base_url = base_url.value
         else:
             self.base_url = base_url
@@ -292,7 +292,7 @@ def logout(self) -> None:
         if not self.access_token:
             return None
 
-        query_url = NBIA_ENDPOINTS.LOGOUT_URL.value
+        query_url = NBIA_BASE_URLS.LOGOUT_URL.value
         response = requests.get(query_url, headers=self.api_headers)
         response.raise_for_status()
 

src/nbiatoolkit/nbia.py

@@ -11,6 +11,7 @@
 from logging import Logger
 from .utils import (
     NBIA_ENDPOINTS,
+    NBIA_BASE_URLS,
     validateMD5,
     clean_html,
     convertMillis,
@@ -64,7 +65,7 @@ def downloadSingleSeries(
     filePattern: str,
     overwrite: bool,
     api_headers: dict[str, str],
-    base_url: NBIA_ENDPOINTS,
+    base_url: NBIA_BASE_URLS,
     log: Logger,
 ):
     """
@@ -123,12 +124,16 @@ def downloadSingleSeries(
 
 
 class NBIAClient:
-    """
-    The NBIAClient class is a wrapper around the NBIA REST API. It provides
-    methods to query the API and download series.
+    """A client for interacting with the NBIA API.
+
+    The NBIAClient class provides a high-level interface for querying the NBIA API and downloading DICOM series.
 
-    The default authentication uses the guest account. If you have a username
-    and password, you can pass them to the constructor.
+    Attributes:
+        OAuth_client (OAuth2): The OAuth2 client used for authentication.
+        headers (dict[str, str]): The API headers.
+        base_url (NBIA_ENDPOINTS): The base URL for API requests.
+        logger (Logger): The logger for logging client events.
+        return_type (str): The current return type for API responses.
     """
 
     def __init__(
@@ -152,7 +157,7 @@ def __init__(
             "Content-Type": "application/json",
         }
 
-        self._base_url: NBIA_ENDPOINTS = NBIA_ENDPOINTS.NBIA
+        self._base_url: NBIA_BASE_URLS = NBIA_BASE_URLS.NBIA
         self._return_type: ReturnType = (
             return_type
             if isinstance(return_type, ReturnType)
@@ -175,11 +180,11 @@ def headers(self):
 
     # create a setter for the base_url in case user want to use NLST
     @property
-    def base_url(self) -> NBIA_ENDPOINTS:
+    def base_url(self) -> NBIA_BASE_URLS:
         return self._base_url
 
     @base_url.setter
-    def base_url(self, nbia_url: NBIA_ENDPOINTS) -> None:
+    def base_url(self, nbia_url: NBIA_BASE_URLS) -> None:
         self._base_url = nbia_url
 
     @property

src/nbiatoolkit/utils/__init__.py

@@ -1,4 +1,4 @@
-from .nbia_endpoints import NBIA_ENDPOINTS
+from .nbia_endpoints import NBIA_ENDPOINTS, NBIA_BASE_URLS
 from .md5 import validateMD5
 from .parsers import (
     convertMillis,
@@ -10,6 +10,7 @@
 
 __all__ = [
     "NBIA_ENDPOINTS",
+    "NBIA_BASE_URLS",
     "validateMD5",
     "convertMillis",
     "clean_html",

src/nbiatoolkit/utils/nbia_endpoints.py

@@ -1,15 +1,28 @@
 from enum import Enum
 
 
-class NBIA_ENDPOINTS(Enum):
+class NBIA_BASE_URLS(Enum):
     """
-    This enum class defines the NBIA endpoints used in the NBIA toolkit.
+    This enum class defines the NBIA base URLs used in the NBIA toolkit.
     """
 
     NBIA = "https://services.cancerimagingarchive.net/nbia-api/services/"
     NLST = "https://nlst.cancerimagingarchive.net/nbia-api/services/"
     LOGOUT_URL = "https://services.cancerimagingarchive.net/nbia-api/logout"
 
+    # Helper functions
+    def __str__(self):
+        return self.value
+
+    def _format(self):
+        return self.value.split("/")[-1]
+
+
+class NBIA_ENDPOINTS(Enum):
+    """
+    This enum class defines the NBIA endpoints used in the NBIA toolkit.
+    """
+
     GET_COLLECTIONS = "v2/getCollectionValues"
     GET_COLLECTION_PATIENT_COUNT = "getCollectionValuesAndCounts"
     GET_COLLECTION_DESCRIPTIONS = "getCollectionDescriptions"

tests/test_new_query_functionality.py

@@ -35,7 +35,7 @@ def test_nbia_properties(nbia_client2):
     assert "Content-Type" in nbia_client.headers.keys()
     assert nbia_client.headers["Content-Type"] == "application/json"
 
-    assert nbia_client.base_url == NBIA_ENDPOINTS.NBIA
+    assert nbia_client.base_url == NBIA_BASE_URLS.NBIA
 
     assert nbia_client.logger is not None
 

tests/test_tcga_collections_separate.py

@@ -42,9 +42,9 @@ def test_nbia_properties(nbia_context_manager):
 
 
 def test_break(nbia_client_tobreak):
-    assert nbia_client_tobreak.base_url == NBIA_ENDPOINTS.NBIA
-    nbia_client_tobreak.base_url = NBIA_ENDPOINTS.NLST
-    assert nbia_client_tobreak.base_url == NBIA_ENDPOINTS.NLST
+    assert nbia_client_tobreak.base_url == NBIA_BASE_URLS.NBIA
+    nbia_client_tobreak.base_url = NBIA_BASE_URLS.NLST
+    assert nbia_client_tobreak.base_url == NBIA_BASE_URLS.NLST
 
 
 def test_getModalityValues(nbia_client, tcga_collections):