Bump version: 0.16.6-rc.0 → 0.16.6

* 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

.bumpversion.cfg

@@ -1,17 +1,14 @@
 [bumpversion]
-current_version = 0.16.0
+current_version = 0.16.6
 commit = True
-# The below regex details an acceptable version number by naming the groups (major, minor, patch, prerel, and
-# prerelversion) and also specifying the valid values for each group (integers, `\d+`,  for major, minor, patch, and
-# prerelversion and only `rc` as the acceptable value for prerel).
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<prerel>rc)\.(?P<prerelversion>\d+))?
-serialize =
+serialize = 
 	{major}.{minor}.{patch}-{prerel}.{prerelversion}
 	{major}.{minor}.{patch}
 
 [bumpversion:part:prerel]
 optional_value = release
-values =
+values = 
 	rc
 	release
 

client/package-lock.json

@@ -1,6 +1,6 @@
 {
   "name": "cellxgene",
-  "version": "0.16.0",
+  "version": "0.16.6",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {

client/package.json

@@ -1,6 +1,6 @@
 {
   "name": "cellxgene",
-  "version": "0.16.0",
+  "version": "0.16.6",
   "license": "MIT",
   "description": "cellxgene is a web application for the interactive exploration of single cell sequence data.",
   "repository": "https://github.com/chanzuckerberg/cellxgene",

server/__init__.py

@@ -2,7 +2,7 @@ import logging
 import sys
 from server.common.utils.utils import import_plugins
 
-__version__ = "0.16.0"
+__version__ = "0.16.6"
 display_version = "cellxgene v" + __version__
 
 try:

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>=1.16.0
 packaging>=20.0

server/test/unit/auth/test_oauth.py

@@ -63,30 +63,53 @@ def jwks():
     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):
-    def setUp(self):
-        self.dataset_dataroot = FIXTURES_ROOT
-        self.mock_oauth_process = Process(target=launch_mock_oauth)
-        self.mock_oauth_process.start()
+    @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, args=(cls.mock_port,))
+        cls.mock_oauth_process.start()
 
-    def tearDown(self):
-        self.mock_oauth_process.terminate()
+        # 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()
 
     def auth_flow(self, app_config, cookie_key=None):
 
         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

setup.py

@@ -11,7 +11,7 @@ with open("server/requirements-prepare.txt") as fh:
 
 setup(
     name="cellxgene",
-    version="0.16.0",
+    version="0.16.6",
     packages=find_packages(),
     url="https://github.com/chanzuckerberg/cellxgene",
     license="MIT",