tests: new tests

src/nbiatoolkit/auth.py

@@ -113,7 +113,7 @@ def __init__(
         username: str = "nbia_guest",
         password: str = "",
         client_id: str = "NBIA",
-        base_url: Union[str, NBIA_ENDPOINTS] = NBIA_ENDPOINTS.BASE_URL,
+        base_url: Union[str, NBIA_ENDPOINTS] = NBIA_ENDPOINTS.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.BASE_URL
+        base_url : str or NBIA_ENDPOINTS, optional. Default is NBIA_ENDPOINTS.NBIA
 
         """
 

src/nbiatoolkit/nbia.py

@@ -26,22 +26,11 @@
 __version__ = "0.29.2"
 
 
-def get_real_ReturnType(return_type: ReturnType):
-
-    if return_type == ReturnType.LIST:
-        return list
-    elif return_type == ReturnType.DATAFRAME:
-        return pd.DataFrame
-
-
 # function that takes a list of dictionaries and returns either a list or a dataframe
 def conv_response_list(
     response_json: List[dict[Any, Any]], return_type: ReturnType = ReturnType.LIST
 ) -> List[dict[Any, Any]] | pd.DataFrame:
 
-    if isinstance(response_json, bytes):
-        return response_json
-
     assert isinstance(response_json, list), "The response JSON must be a list"
 
     if return_type == ReturnType.LIST:
@@ -59,8 +48,6 @@ class NBIAClient:
 
     The default authentication uses the guest account. If you have a username
     and password, you can pass them to the constructor.
-
-    TODO:: Add docstring
     """
 
     def __init__(
@@ -79,17 +66,12 @@ def __init__(
         self._log.debug("Setting up OAuth2 client... with username %s", username)
         self._oauth2_client = OAuth2(username=username, password=password)
 
-        try:
-            self._api_headers = {
-                "Authorization": f"Bearer {self._oauth2_client.access_token}",
-                "Content-Type": "application/json",
-            }
-        except Exception as e:
-            self._log.error("Error retrieving access token: %s", e)
-            self._api_headers = None
-            raise e
+        self._api_headers: dict[str, str] = {
+            "Authorization": f"Bearer {self._oauth2_client.access_token}",
+            "Content-Type": "application/json",
+        }
 
-        self._base_url: NBIA_ENDPOINTS = NBIA_ENDPOINTS.BASE_URL
+        self._base_url: NBIA_ENDPOINTS = NBIA_ENDPOINTS.NBIA
         self._return_type: ReturnType = (
             return_type
             if isinstance(return_type, ReturnType)

src/nbiatoolkit/utils/nbia_endpoints.py

@@ -6,8 +6,8 @@ class NBIA_ENDPOINTS(Enum):
     This enum class defines the NBIA endpoints used in the NBIA toolkit.
     """
 
-    BASE_URL = "https://services.cancerimagingarchive.net/nbia-api/services/"
-    NLST_URL = "https://nlst.cancerimagingarchive.net/nbia-api/services/"
+    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"
 
     GET_COLLECTIONS = "v2/getCollectionValues"

tests/deprecated_test_nbia.py

@@ -17,12 +17,6 @@ def nbia_client():
     return nbia
 
 
-@pytest.fixture(scope="session")
-def nbia_client_bad_username():
-    nbia = NBIAClient(username="bad_username", password="bad_password")
-    return nbia
-
-
 @pytest.fixture(scope="session")
 def nbia_collections(nbia_client):
     collections = nbia_client.getCollections()

tests/test_new_query_functionality.py

@@ -1,7 +1,7 @@
 import pytest
 
 from src.nbiatoolkit import NBIAClient
-
+from src.nbiatoolkit.utils import *
 import pandas as pd
 
 
@@ -11,6 +11,12 @@ def nbia_client():
     return nbia_client
 
 
+@pytest.fixture(scope="session")
+def nbia_client_bad_username():
+    nbia = NBIAClient(username="bad_username", password="bad_password")
+    return nbia
+
+
 @pytest.fixture(scope="session")
 def tcga_collections(nbia_client):
     tcga_collections = nbia_client.getCollections(prefix="TCGA")
@@ -25,6 +31,16 @@ def tcga_collection_df(nbia_client):
     return tcga_collection_df
 
 
+def test_change_base_url(nbia_client):
+    nbia_client.base_url = NBIA_ENDPOINTS.NLST
+    assert nbia_client.base_url == NBIA_ENDPOINTS.NLST
+
+
+def test_failed_NBIA_CLIENT():
+    with pytest.raises(Exception) as e:
+        nbia = NBIAClient(username="bad_username", password="bad_password")
+
+
 def test_tcga_collection(tcga_collections):
     assert isinstance(tcga_collections, list)
     assert len(tcga_collections) > 1