tests: fix breaking and turn that into new test

tests/test_nbia_series_functions.py

@@ -1,8 +1,6 @@
 import pytest
-from nbiatoolkit import nbia
 
 from src.nbiatoolkit import NBIAClient
-from src.nbiatoolkit.auth import OAuth2
 from src.nbiatoolkit.utils import *
 import pandas as pd
 
@@ -29,7 +27,55 @@ def tcga_studies(nbia_client):
     return tcga_studies
 
 
+@pytest.fixture(scope="session")
+def nbia_patients_df(nbia_client: NBIAClient):
+    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: NBIAClient, nbia_patients_df):
+    nbia_collections_by_colMoldality = nbia_client.getPatientsByCollectionAndModality(
+        Collection="TCGA-KIRC", Modality="MR"
+    )
+    return nbia_collections_by_colMoldality
+
+
 def test_tcga_studies(tcga_studies):
 
     assert isinstance(tcga_studies, list)
     assert len(tcga_studies) > 0
+
+
+def test_failed_getNewPatients(nbia_client):
+    with pytest.raises(Exception) as e:
+        # collection isntead of Collection
+        nbia_client.getNewPatients(collection="TCGA", Date="2022/12/06")
+
+    with pytest.raises(Exception) as e:
+        # collection isntead of Collection
+        nbia_client.getNewPatients(
+            collection="TCGA", return_type="dataframe", Date="2022/12/06"
+        )
+
+
+def test_getNewPatients(nbia_patients_df):
+
+    assert isinstance(nbia_patients_df, pd.DataFrame)
+    assert len(nbia_patients_df) > 1
+    expected_cols: list[str] = [
+        "PatientId",
+        "PatientName",
+        "PatientSex",
+        "Collection",
+        "Phantom",
+        "SpeciesCode",
+        "Species",
+    ]
+
+
+def test_nbia_collections_by_colMoldality(nbia_collections_by_colMoldality):
+    assert isinstance(nbia_collections_by_colMoldality, list)
+    assert len(nbia_collections_by_colMoldality) > 1

tests/test_new_query_functionality.py

@@ -12,15 +12,6 @@ def nbia_client():
     return nbia_client
 
 
-@pytest.fixture(scope="session")
-def tcga_collections(nbia_client):
-    tcga_collections = nbia_client.getCollections(prefix="TCGA")
-    tcga_collection_df = nbia_client.getCollections(
-        prefix="TCGA", return_type="dataframe"
-    )
-    return (tcga_collection_df, tcga_collections)
-
-
 @pytest.fixture(scope="session")
 def tcga_patients(nbia_client):
 
@@ -29,22 +20,6 @@ def tcga_patients(nbia_client):
     return tcga_patients
 
 
-@pytest.fixture(scope="session")
-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: NBIAClient, nbia_patients_df):
-    nbia_collections_by_colMoldality = nbia_client.getPatientsByCollectionAndModality(
-        Collection="TCGA-KIRC", Modality="MR"
-    )
-    return nbia_collections_by_colMoldality
-
-
 def test_nbia_properties(nbia_client):
     assert isinstance(nbia_client.OAuth_client, OAuth2)
     assert isinstance(nbia_client.headers, dict)
@@ -53,22 +28,10 @@ def test_nbia_properties(nbia_client):
     assert nbia_client.headers["Content-Type"] == "application/json"
 
     assert nbia_client.base_url == NBIA_ENDPOINTS.NBIA
-    nbia_client.base_url = NBIA_ENDPOINTS.NLST
-    assert nbia_client.base_url == NBIA_ENDPOINTS.NLST
 
     assert nbia_client.logger is not None
 
 
-def test_tcga_collection(tcga_collections):
-    tcga_collections_df, tcga_collections1 = tcga_collections
-    assert isinstance(tcga_collections1, list)
-    assert len(tcga_collections1) > 1
-
-    assert isinstance(tcga_collections_df, pd.DataFrame)
-    assert "Collection" in tcga_collections_df.columns
-    assert len(tcga_collections_df) > 1
-
-
 def test_tcga_collection_description(nbia_client: NBIAClient):
     tcga_collection_description_df = nbia_client.getCollectionDescriptions(
         collectionName="TCGA-KIRC", return_type="dataframe"
@@ -84,22 +47,6 @@ def test_tcga_collection_description(nbia_client: NBIAClient):
     assert len(tcga_collection_description_df) == 1
 
 
-def test_getModalityValues(nbia_client, tcga_collections):
-    tcga_collections_df, tcga_collections = tcga_collections
-    modality_values = nbia_client.getModalityValues(
-        Collection=tcga_collections[0]["Collection"]
-    )
-    assert isinstance(modality_values, list)
-    assert len(modality_values) > 1
-
-    modality_values_df = nbia_client.getModalityValues(
-        Collection=tcga_collections[0]["Collection"], return_type="dataframe"
-    )
-    assert isinstance(modality_values_df, pd.DataFrame)
-    assert "Modality" in modality_values_df.columns
-    assert len(modality_values_df) > 1
-
-
 def test_failed_getModalityValues(nbia_client):
     with pytest.raises(Exception) as e:
         # collection isntead of Collection
@@ -114,35 +61,3 @@ def test_getPatients(nbia_client, tcga_patients):
 
     assert isinstance(tcga_patients, list)
     assert len(tcga_patients) > 1
-
-
-def test_getNewPatients(nbia_patients_df):
-
-    assert isinstance(nbia_patients_df, pd.DataFrame)
-    assert len(nbia_patients_df) > 1
-    expected_cols: list[str] = [
-        "PatientId",
-        "PatientName",
-        "PatientSex",
-        "Collection",
-        "Phantom",
-        "SpeciesCode",
-        "Species",
-    ]
-
-
-def test_failed_getNewPatients(nbia_client):
-    with pytest.raises(Exception) as e:
-        # collection isntead of Collection
-        nbia_client.getNewPatients(collection="TCGA", Date="2022/12/06")
-
-    with pytest.raises(Exception) as e:
-        # collection isntead of Collection
-        nbia_client.getNewPatients(
-            collection="TCGA", return_type="dataframe", Date="2022/12/06"
-        )
-
-
-def test_nbia_collections_by_colMoldality(nbia_collections_by_colMoldality):
-    assert isinstance(nbia_collections_by_colMoldality, list)
-    assert len(nbia_collections_by_colMoldality) > 1

tests/test_tcga_collections_separate.py

@@ -0,0 +1,59 @@
+from math import log
+import pytest
+from src.nbiatoolkit import NBIAClient
+from src.nbiatoolkit.auth import OAuth2
+from src.nbiatoolkit.utils import *
+import pandas as pd
+
+
+@pytest.fixture(scope="session")
+def nbia_client():
+    nbia_client = NBIAClient(log_level="DEBUG")
+    return nbia_client
+
+
+@pytest.fixture(scope="session")
+def nbia_client_tobreak():
+    nbia_client = NBIAClient(log_level="DEBUG")
+    return nbia_client
+
+
+@pytest.fixture(scope="session")
+def tcga_collections(nbia_client):
+    tcga_collections = nbia_client.getCollections(prefix="TCGA")
+    tcga_collection_df = nbia_client.getCollections(
+        prefix="TCGA", return_type="dataframe"
+    )
+    return (tcga_collection_df, tcga_collections)
+
+
+def test_break(nbia_client_tobreak):
+    assert nbia_client.base_url == NBIA_ENDPOINTS.NBIA
+    nbia_client.base_url = NBIA_ENDPOINTS.NLST
+    assert nbia_client.base_url == NBIA_ENDPOINTS.NLST
+
+
+def test_getModalityValues(nbia_client, tcga_collections):
+    tcga_collections_df, tcga_collections = tcga_collections
+    modality_values = nbia_client.getModalityValues(
+        Collection=tcga_collections[0]["Collection"]
+    )
+    assert isinstance(modality_values, list)
+    assert len(modality_values) > 1
+
+    modality_values_df = nbia_client.getModalityValues(
+        Collection=tcga_collections[0]["Collection"], return_type="dataframe"
+    )
+    assert isinstance(modality_values_df, pd.DataFrame)
+    assert "Modality" in modality_values_df.columns
+    assert len(modality_values_df) > 1
+
+
+def test_tcga_collection(tcga_collections):
+    tcga_collections_df, tcga_collections1 = tcga_collections
+    assert isinstance(tcga_collections1, list)
+    assert len(tcga_collections1) > 1
+
+    assert isinstance(tcga_collections_df, pd.DataFrame)
+    assert "Collection" in tcga_collections_df.columns
+    assert len(tcga_collections_df) > 1