[2/2] Upgrade direct Python dependencies (#6511)

Require code updates to be compatible with the dependency updates

src/azul/plugins/metadata/hca/indexer/aggregate.py

@@ -49,7 +49,6 @@ class HCAAggregate(Aggregate):
 
     @cached_property
     def cell_count(self) -> int:
-        cs: JSON
         return sum(cs['total_estimated_cells']
                    for cs in self.contents['cell_suspensions']
                    if cs['total_estimated_cells'] is not None)

test/azul_test_case.py

@@ -147,6 +147,15 @@ class RE(str):
                     'The \'body\' parameter is deprecated for the \'.*\' API '
                     'and will be removed in .*. Instead use .*'
                 ),
+                'validate_spec shortcut is deprecated. Use validate instead.',
+                (
+                    'Automatically retrieving remote references can be a security vulnerability and'
+                    ' is discouraged by the JSON Schema specifications. Relying on this behavior is'
+                    ' deprecated and will shortly become an error. If you are sure you want to '
+                    'remotely retrieve your reference and that it is safe to do so, you can find '
+                    'instructions for doing so via referencing.Registry in the referencing '
+                    'documentation (https://referencing.readthedocs.org).'
+                )
             },
             UserWarning: {
                 'https://github.com/DataBiosphere/azul/issues/2114',
@@ -210,7 +219,7 @@ def addPatch(self, instance: patch) -> None:
         # Moto mock's stop() method has the drastic effect of resetting the
         # model class attributes that are used to track model instances so that
         # they can later be cleaned up when the backend is reset.
-        if isinstance(instance, moto.BaseMockAWS):
+        if isinstance(instance, moto.core.models.MockAWS):
             cleanup = partial(instance.stop, remove_data=False)
         else:
             cleanup = instance.stop

test/dynamodb_test_case.py

@@ -7,7 +7,7 @@
 )
 
 from moto import (
-    mock_dynamodb,
+    mock_aws,
 )
 from mypy_boto3_dynamodb import (
     DynamoDBClient,
@@ -46,7 +46,7 @@ def dynamodb(self) -> DynamoDBClient:
 
     def setUp(self):
         super().setUp()
-        self.addPatch(mock_dynamodb())
+        self.addPatch(mock_aws())
         self.dynamodb.create_table(TableName=self._dynamodb_table_name(),
                                    BillingMode='PAY_PER_REQUEST',
                                    AttributeDefinitions=[

test/health_check_test_case.py

@@ -23,8 +23,7 @@
     furl,
 )
 from moto import (
-    mock_sqs,
-    mock_sts,
+    mock_aws,
 )
 import requests
 import responses
@@ -86,8 +85,7 @@ def test_validation(self):
             response = requests.get(str(self.base_url.set(path=('health', path))))
             self.assertEqual(400, response.status_code)
 
-    @mock_sts
-    @mock_sqs
+    @mock_aws
     def test_health_all_ok(self):
         self._create_mock_queues()
         with self._mock():
@@ -102,8 +100,7 @@ def test_health_all_ok(self):
             **self._expected_progress()
         }, response.json())
 
-    @mock_sts
-    @mock_sqs
+    @mock_aws
     def test_health_endpoint_keys(self):
         expected = {
             keys: {
@@ -126,8 +123,7 @@ def test_health_endpoint_keys(self):
                 self.assertEqual(200, response.status_code)
                 self.assertEqual(expected_response, response.json())
 
-    @mock_sts
-    @mock_sqs
+    @mock_aws
     def test_cached_health(self):
         # No health object is available in S3 bucket, yielding an error
         with self._mock():
@@ -180,8 +176,7 @@ def _expected_health(self,
                          ) -> MutableJSON:
         raise NotImplementedError
 
-    @mock_sts
-    @mock_sqs
+    @mock_aws
     def test_elasticsearch_down(self):
         self._create_mock_queues()
         mock_endpoint = ('7c9f2ddb-74ca-46a3-9438-24ce1fe7050e.com', 80)
@@ -204,8 +199,7 @@ def _expected_queues(self, *, up: bool) -> MutableJSON:
                         }
                     } if up else {
                         'up': False,
-                        'error': 'The specified queue does not exist for'
-                                 ' this wsdl version.'
+                        'error': 'The specified queue does not exist.'
                     }
                     for queue_name in config.all_queue_names
                 })

test/indexer/test_health_check.py

@@ -1,6 +1,5 @@
 from moto import (
-    mock_sqs,
-    mock_sts,
+    mock_aws,
 )
 
 from azul.logging import (
@@ -39,8 +38,7 @@ def _expected_health(self,
             **self._expected_progress()
         }
 
-    @mock_sts
-    @mock_sqs
+    @mock_aws
     def test_queues_down(self):
         with self._mock():
             response = self._test('/health/fast')

test/indexer/test_indexer_controller.py

@@ -25,8 +25,7 @@
     one,
 )
 from moto import (
-    mock_sqs,
-    mock_sts,
+    mock_aws,
 )
 
 from azul import (
@@ -76,8 +75,7 @@ def setUpModule():
     configure_test_logging(log)
 
 
-@mock_sts
-@mock_sqs
+@mock_aws
 class TestIndexController(DCP1IndexerTestCase, SqsTestCase):
     partition_prefix_length = 0
 

test/indexer/test_notifications.py

@@ -6,8 +6,7 @@
 )
 
 from moto import (
-    mock_sqs,
-    mock_sts,
+    mock_aws,
 )
 import requests
 
@@ -39,8 +38,7 @@ class TestValidNotificationRequests(LocalAppTestCase,
     def lambda_name(cls) -> str:
         return 'indexer'
 
-    @mock_sts
-    @mock_sqs
+    @mock_aws
     def test_successful_notifications(self):
         self._create_mock_notifications_queue()
         body = {
@@ -55,8 +53,7 @@ def test_successful_notifications(self):
                 self.assertEqual(202, response.status_code)
                 self.assertEqual('', response.text)
 
-    @mock_sts
-    @mock_sqs
+    @mock_aws
     def test_invalid_notifications(self):
         bodies = {
             'Missing body': {},
@@ -108,8 +105,7 @@ def test_invalid_notifications(self):
                         response = self._test(body, delete, valid_auth=True)
                         self.assertEqual(400, response.status_code)
 
-    @mock_sts
-    @mock_sqs
+    @mock_aws
     def test_invalid_auth_for_notification_request(self):
         self._create_mock_notifications_queue()
         body = {

test/service/__init__.py

@@ -29,8 +29,7 @@
     one,
 )
 from moto import (
-    mock_s3,
-    mock_sts,
+    mock_aws,
 )
 from mypy_boto3_s3.client import (
     S3Client,
@@ -216,8 +215,7 @@ def _s3(self) -> S3Client:
 
     def setUp(self) -> None:
         super().setUp()
-        self.addPatch(mock_sts())
-        self.addPatch(mock_s3())
+        self.addPatch(mock_aws())
 
     def _create_test_bucket(self, bucket_name: str):
         assert config.region in get_args(BucketLocationConstraintType)

test/service/test_app_logging.py

@@ -45,7 +45,7 @@ def test_request_logs(self):
                     logs = [(r.levelno, r.getMessage()) for r in logs.records]
                     headers = {
                         'host': url.netloc,
-                        'user-agent': 'python-requests/2.32.2',
+                        'user-agent': 'python-requests/2.32.3',
                         'accept-encoding': 'gzip, deflate, br',
                         'accept': '*/*',
                         'connection': 'keep-alive',

test/service/test_health_check.py

@@ -1,6 +1,5 @@
 from moto import (
-    mock_sqs,
-    mock_sts,
+    mock_aws,
 )
 
 from azul.logging import (
@@ -38,8 +37,7 @@ def _expected_health(self,
             **self._expected_api_endpoints(up=endpoints_up),
         }
 
-    @mock_sts
-    @mock_sqs
+    @mock_aws
     def test_all_api_endpoints_down(self):
         self._create_mock_queues()
         with self._mock(endpoints_up=False):

test/service/test_manifest_async.py

@@ -23,7 +23,7 @@
     furl,
 )
 from moto import (
-    mock_sts,
+    mock_aws,
 )
 import requests
 import responses
@@ -150,7 +150,7 @@ def lambda_name(cls) -> str:
 
     execution_id = b'42'
 
-    @mock_sts
+    @mock_aws
     @mock.patch.object(AsyncManifestService, '_sfn')
     @mock.patch.object(ManifestService, 'get_manifest')
     @mock.patch.object(ManifestService, 'get_cached_manifest')

test/service/test_source_cache.py

@@ -7,7 +7,7 @@
 )
 
 from moto import (
-    mock_dynamodb,
+    mock_aws,
 )
 from mypy_boto3_dynamodb.literals import (
     ScalarAttributeTypeType,
@@ -23,7 +23,7 @@
 )
 
 
-@mock_dynamodb
+@mock_aws
 class TestSourceCache(DynamoDBTestCase):
 
     def _dynamodb_table_name(self) -> str:

test/service/test_version_service.py

@@ -1,5 +1,5 @@
 from moto import (
-    mock_dynamodb,
+    mock_aws,
 )
 
 from azul.logging import (
@@ -19,7 +19,7 @@ def setUpModule():
     configure_test_logging()
 
 
-@mock_dynamodb
+@mock_aws
 class TestVersionService(VersionTableTestCase):
 
     def setUp(self):

test/test_app_logging.py

@@ -81,7 +81,7 @@ def fail():
                     self.assertEqual(len(azul_log.output), 3)
                     headers = {
                         'host': f'{host}:{port}',
-                        'user-agent': 'python-requests/2.32.2',
+                        'user-agent': 'python-requests/2.32.3',
                         'accept-encoding': 'gzip, deflate, br',
                         'accept': '*/*',
                         'connection': 'keep-alive'