tests: add a few tests

tests/test_nbia_series_functions.py

@@ -19,3 +19,17 @@ def tcga_series(nbia_client):
         Collection="TCGA-KIRC", PatientID="TCGA-BP-4989"
     )
     return tcga_series
+
+
+@pytest.fixture(scope="session")
+def tcga_studies(nbia_client):
+    tcga_studies = nbia_client.getStudies(
+        Collection="TCGA-KIRC", PatientID="TCGA-BP-4989"
+    )
+    return tcga_studies
+
+
+def test_tcga_studies(tcga_studies):
+
+    assert isinstance(tcga_studies, list)
+    assert len(tcga_studies) > 0

tests/test_new_query_functionality.py

@@ -1,6 +1,4 @@
 import pytest
-from nbiatoolkit import nbia
-
 from src.nbiatoolkit import NBIAClient
 from src.nbiatoolkit.auth import OAuth2
 from src.nbiatoolkit.utils import *
@@ -13,12 +11,6 @@ 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")
@@ -37,15 +29,15 @@ def tcga_patients(nbia_client):
 
 
 @pytest.fixture(scope="session")
-def nbia_patients_df(nbia_client):
+def nbia_patients_df(nbia_client: NBIAClient, tcga_patients):
     nbia_patients_df = nbia_client.getNewPatients(
         Collection="CMB-LCA", return_type="dataframe", Date="2022/12/06"
     )
     return nbia_patients_df
 
 
 @pytest.fixture(scope="session")
-def nbia_collections_by_colMoldality(nbia_client):
+def nbia_collections_by_colMoldality(nbia_client: NBIAClient, nbia_patients_df):
     nbia_collections_by_colMoldality = nbia_client.getPatientsByCollectionAndModality(
         Collection="TCGA-KIRC", Modality="MR"
     )