Updates due dependency version changes. (#1960)

* Updates due dependency version changes.

h5py recently changes and now values once returned as str are now returned as bytes.
This would have caused a much larger change, so instead the version is restricted to <3.0.0.

This caused the bulk of the testing failues.
A few other changes were needed to make a few other tests pass.

 #1959

server/common/annotations/hosted_tiledb.py

@@ -34,6 +34,12 @@ class AnnotationsHostedTileDB(Annotations):
                 f"{unsanitary_original_category_names} are not valid category names, please resubmit"
             )
 
+    def get_user_name(self):
+        return current_app.auth.get_user_name()
+
+    def get_user_id(self):
+        return current_app.auth.get_user_id()
+
     def is_safe_collection_name(self, name):
         """
         return true if this is a safe collection name
@@ -48,7 +54,7 @@ class AnnotationsHostedTileDB(Annotations):
         self.CXG_ANNO_COLLECTION = name
 
     def read_labels(self, data_adaptor):
-        user_id = current_app.auth.get_user_id()
+        user_id = self.get_user_id()
         if user_id is None:
             return
         dataset_name = data_adaptor.get_location()
@@ -103,8 +109,8 @@ class AnnotationsHostedTileDB(Annotations):
         return new_df
 
     def write_labels(self, df, data_adaptor):
-        auth_user_id = current_app.auth.get_user_id()
-        user_name = current_app.auth.get_user_name()
+        auth_user_id = self.get_user_id()
+        user_name = self.get_user_name()
         timestamp = time.time()
         dataset_location = data_adaptor.get_location()
         dataset_id = self.db.get_or_create_dataset(dataset_location)

server/requirements.txt

@@ -12,6 +12,7 @@ flatbuffers>=1.11.0
 flatten-dict>=0.2.0
 fsspec>=0.4.4,<0.8.0
 gunicorn>=20.0.4
+h5py<3.0.0 # h5py returns bytes instead of str, which breaks many assumptions
 numba>=0.49.1
 numpy>=1.15.0
 packaging>=20.0

server/test/unit/auth/test_oauth.py

@@ -62,22 +62,44 @@ def jwks():
     data = dict(alg="RS256", kty="RSA", use="sig", kid="fake_kid",)
     return make_response(jsonify(dict(keys=[data])))
 
-# The port that the mock oauth server will listen on
-PORT = random.randint(10000, 12000)
-
 
 # function to launch the mock oauth server
-def launch_mock_oauth():
-    mock_oauth_app.run(port=PORT)
+def launch_mock_oauth(mock_port):
+    mock_oauth_app.run(port=mock_port)
 
 
 class AuthTest(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
+        # The port that the mock oauth server will listen on
+        cls.mock_port = random.randint(10000, 12000)
         cls.dataset_dataroot = FIXTURES_ROOT
-        cls.mock_oauth_process = Process(target=launch_mock_oauth)
+        cls.mock_oauth_process = Process(target=launch_mock_oauth, args=(cls.mock_port,))
         cls.mock_oauth_process.start()
 
+        # Verify that the mock oauth server is ready (accepting requests) before starting the tests.
+
+        # The following lines are polling until the mock server is ready.
+        # The issue is we are starting a mock oauth server, then we are starting a cellxgene server,
+        # which will start making requests to the mock oauth server.
+        # So there is a race condition because the mock oauth server needs to be ready before it gets requests.
+        # We check to see if it is ready, and if not we wait 1 second, then try again.
+        # If it gets to 5 seconds, which is shouldn't, we assume something has gone wrong and fail the test.
+        server_okay = False
+        for _ in range(5):
+            try:
+                response = requests.get(f"http://localhost:{cls.mock_port}/.well-known/jwks.json")
+                if response.status_code == 200:
+                    server_okay = True
+                    break
+            except:  # noqa: E722
+                pass
+
+            # wait one second and try again
+            time.sleep(1)
+
+        assert(server_okay)
+
     @classmethod
     def tearDownClass(cls):
         cls.mock_oauth_process.terminate()
@@ -87,7 +109,7 @@ class AuthTest(unittest.TestCase):
         app_config.update_server_config(
             app__api_base_url="local",
             authentication__type="oauth",
-            authentication__params_oauth__oauth_api_base_url=f"http://localhost:{PORT}",
+            authentication__params_oauth__oauth_api_base_url=f"http://localhost:{self.mock_port}",
             authentication__params_oauth__client_id="mock_client_id",
             authentication__params_oauth__client_secret="mock_client_secret",
             authentication__params_oauth__jwt_decode_options={"verify_signature": False, "verify_iss": False},

server/test/unit/common/test_writable_annotation.py

@@ -129,9 +129,11 @@ class WritableTileDBStoredAnnotationTest(unittest.TestCase):
             with self.assertRaises(KeyError):
                 self.annotation_put_fbs(fbs_bad)
 
-    @patch("server.common.annotations.hosted_tiledb.current_app")
-    def test_write_labels_stores_df_as_tiledb_array(self, mock_user_id):
-        mock_user_id.auth.get_user_id.return_value = "1234"
+    @patch("server.common.annotations.hosted_tiledb.AnnotationsHostedTileDB.get_user_id")
+    @patch("server.common.annotations.hosted_tiledb.AnnotationsHostedTileDB.get_user_name")
+    def test_write_labels_stores_df_as_tiledb_array(self, mock_user_name, mock_user_id):
+        mock_user_id.return_value = "1234"
+        mock_user_name.return_value = "user1234"
         self.annotations.write_labels(self.df, self.data)
         # get uri
         dataset_id = self.db.query([CellxGeneDataset], [CellxGeneDataset.name == self.data.get_location()])[0].id