refactor nbia client and add tests

driver.py

@@ -9,13 +9,19 @@
 PASSWORD = "q6mJyLD8cPeGTwg!"
 
 
-client = NBIAClient(username=USERNAME, password=PASSWORD)
+client = NBIAClient(
+    username=USERNAME, 
+    password=PASSWORD,
+    log_level="DEBUG")
+
 series = client.getSeries(Collection="RADCURE")
 
 seriesList = [_["SeriesInstanceUID"] for _ in series]
 seriesList = seriesList[0:5]
 
 
+
+
 def download(series) -> bool:
     response = client.downloadSeries(
         SeriesInstanceUID = series,

src/nbiatoolkit/nbia.py

@@ -21,7 +21,10 @@ def __init__(self,
 
         # Setup logger
         self.logger = setup_logger(
-            name = "NBIAClient", console_logging=True, log_level=log_level)
+            name = "NBIAClient", 
+            console_logging=True, 
+            log_level=log_level,
+            log_file = None)
 
         # Setup OAuth2 client
         self.logger.debug("Setting up OAuth2 client... with username %s", username)
@@ -33,7 +36,7 @@ def query_api(self, endpoint: NBIA_ENDPOINTS, params: dict = {}) -> dict:
         query_url = base_url + endpoint.value
 
         self.logger.debug("Querying API endpoint: %s", query_url)
-        self.logger.debug("API headers: %s", (self._createDebugURL(endpoint, params)))
+        # self.logger.debug("API headers: %s", (self._createDebugURL(endpoint, params)))
 
         try:
             response = requests.get(

tests/test_nbia.py

@@ -13,13 +13,24 @@ 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()
+    return collections
+
+@pytest.fixture(scope="session")
+def nbia_patients(nbia_client, nbia_collections):
+    patients = nbia_client.getPatients(
+        collection=nbia_collections[0], modality = "CT")
+    return patients
+
 def test_nbiaclient_access_token(nbia_client):
     assert nbia_client.api_headers is not None
 
-def test_getCollections(nbia_client):
-    collections = nbia_client.getCollections()
-    assert isinstance(collections, list)
-    assert len(collections) > 0
+def test_getCollections(nbia_collections):
+    assert isinstance(nbia_collections, list)
+    assert len(nbia_collections) > 0
 
 def test_getBodyPartCounts_all(nbia_client):
     bodyparts = nbia_client.getBodyPartCounts()
@@ -48,10 +59,35 @@ def test_getCollectionPatientCount(nbia_client):
     assert "PatientCount" in patientCount[0]
     assert int(patientCount[0]["PatientCount"]) > 0
 
-def test_getPatients(nbia_client):
-    patientList = nbia_client.getPatients("LIDC-IDRI", "CT")
-    assert isinstance(patientList, list)
-    assert len(patientList) > 0
-    assert isinstance(patientList[0], str)
-    assert len(patientList[0]) > 0
-
+def test_getPatients(nbia_patients):
+    assert isinstance(nbia_patients, list)
+    assert len(nbia_patients) > 0
+    assert isinstance(nbia_patients[0], str)
+    assert len(nbia_patients[0]) > 0
+
+@pytest.mark.getSeries
+def test_getSeries(nbia_client, nbia_collections, nbia_patients):
+    seriesList = nbia_client.getSeries(
+        Collection=nbia_collections[0],
+        PatientID=nbia_patients[0],
+        Modality="CT"
+    )
+    assert seriesList is not None
+    assert isinstance(seriesList, list)
+    assert len(seriesList) > 0
+    assert isinstance(seriesList[0], dict)
+
+@pytest.mark.getSeries
+def test_fail_getSeries(nbia_client, nbia_collections, nbia_patients):
+    with pytest.raises(Exception):
+        seriesList = nbia_client.getSeries(
+            Collection=nbia_collections[0],
+            PatientID=nbia_patients[0],
+            Modality="CT",
+            SeriesInstanceUID="bad_series_uid"
+        )
+        assert seriesList is not None
+        assert isinstance(seriesList, list)
+        assert len(seriesList) > 0
+        assert isinstance(seriesList[0], dict)
+