Change loop_scope to module ...

Due to conflicting issues between more than one event loop with these
tests I've done two things.

1) Removed tests that have external querying from the test group. While
   it will make the unit tests less robust, having external queries was
   always going to be slighly flakier. This way the core tests leverage
   the built-in testing clients for exercising the annotator as a web
   service through the endpoints. The annotator as a standalone library
   is important but comes second to that
2) Set the loop scope to module to allow for the event loop to exist for
   groups of tests that are semantically similar.

tests/fixtures/application.py

@@ -13,8 +13,7 @@ def test_annotator() -> sanic.Sanic:
     Generate an application instance from the biothings_annotator
     """
     default_configuration = load_configuration()
-    default_configuration["application"]["runtime"]["debug"] = False
-    default_configuration["application"]["runtime"]["port"] = 7777
+    default_configuration["application"]["runtime"]["debug"] = True
     application = build_application(default_configuration)
     TestManager(application)
-    return application
+    yield application

tests/test_annotation_performance.py

@@ -29,7 +29,7 @@
 
 
 @pytest.mark.performance
-@pytest.mark.asyncio(scope="module")
+@pytest.mark.asyncio(loop_scope="module")
 @pytest.mark.parametrize("data_store", ["cleaned_annotator_logs.json"])
 async def test_integration_server_responses(
     temporary_data_storage: Union[str, Path],
@@ -281,7 +281,7 @@ def test_ara_integration_trapi_requests(
 
 
 @pytest.mark.performance
-@pytest.mark.asyncio(scope="module")
+@pytest.mark.asyncio(loop_scope="module")
 @pytest.mark.parametrize("data_store", ["cleaned_annotator_logs.json"])
 async def test_asynchronous_bulk_requests(
     temporary_data_storage: Union[str, Path],
@@ -312,7 +312,7 @@ async def test_asynchronous_bulk_requests(
 
 
 @pytest.mark.performance
-@pytest.mark.asyncio(scope="module")
+@pytest.mark.asyncio(loop_scope="module")
 @pytest.mark.parametrize(
     "data_store",
     [

tests/test_application_configuration.py

@@ -54,7 +54,6 @@ def test_environment_configuration(host: str):
 
             assert client.url == f"{annotator_instance.api_host}/{endpoint}"
             assert ANNOTATOR_CLIENTS[node_type]["client"]["instance"] == client
-            breakpoint()
     finally:
         if os.environ.get("SERVICE_PROVIDER_API_HOST", None) is not None:
             del os.environ["SERVICE_PROVIDER_API_HOST"]

tests/test_application_endpoints.py

@@ -12,7 +12,7 @@
 
 
 @pytest.mark.unit
-@pytest.mark.asyncio(scope="module")
+@pytest.mark.asyncio(loop_scope="module")
 @pytest.mark.parametrize("endpoint", ["/status/"])
 async def test_status_get(test_annotator: sanic.Sanic, endpoint: str):
     """
@@ -38,7 +38,7 @@ async def test_status_get(test_annotator: sanic.Sanic, endpoint: str):
 
 
 @pytest.mark.unit
-@pytest.mark.asyncio(scope="module")
+@pytest.mark.asyncio(loop_scope="module")
 @pytest.mark.parametrize("endpoint", ["/status/"])
 async def test_status_head(test_annotator: sanic.Sanic, endpoint: str):
     """
@@ -62,7 +62,7 @@ async def test_status_head(test_annotator: sanic.Sanic, endpoint: str):
 
 
 @pytest.mark.unit
-@pytest.mark.asyncio(scope="module")
+@pytest.mark.asyncio(loop_scope="module")
 @pytest.mark.parametrize("endpoint", ["/status/"])
 async def test_status_get_error(test_annotator: sanic.Sanic, endpoint: str):
     """
@@ -89,7 +89,7 @@ async def test_status_get_error(test_annotator: sanic.Sanic, endpoint: str):
 
 
 @pytest.mark.unit
-@pytest.mark.asyncio(scope="module")
+@pytest.mark.asyncio(loop_scope="module")
 @pytest.mark.parametrize("endpoint", ["/status/"])
 async def test_status_get_failed_data_check(test_annotator: sanic.Sanic, endpoint: str):
     """
@@ -117,7 +117,7 @@ async def test_status_get_failed_data_check(test_annotator: sanic.Sanic, endpoin
 
 
 @pytest.mark.unit
-@pytest.mark.asyncio(scope="module")
+@pytest.mark.asyncio(loop_scope="module")
 @pytest.mark.parametrize("endpoint", ["/version/"])
 async def test_version_get_success(test_annotator: sanic.Sanic, endpoint: str):
     """
@@ -146,7 +146,7 @@ async def test_version_get_success(test_annotator: sanic.Sanic, endpoint: str):
 
 
 @pytest.mark.unit
-@pytest.mark.asyncio(scope="module")
+@pytest.mark.asyncio(loop_scope="module")
 @pytest.mark.parametrize("endpoint", ["/version/"])
 async def test_version_get_file_not_found(test_annotator: sanic.Sanic, endpoint: str):
     """
@@ -175,7 +175,7 @@ async def test_version_get_file_not_found(test_annotator: sanic.Sanic, endpoint:
 
 
 @pytest.mark.unit
-@pytest.mark.asyncio(scope="module")
+@pytest.mark.asyncio(loop_scope="module")
 @pytest.mark.parametrize("endpoint", ["/version/"])
 async def test_version_get_exception(test_annotator: sanic.Sanic, endpoint: str):
     """
@@ -204,7 +204,7 @@ async def test_version_get_exception(test_annotator: sanic.Sanic, endpoint: str)
 
 
 @pytest.mark.unit
-@pytest.mark.asyncio(scope="module")
+@pytest.mark.asyncio(loop_scope="module")
 @pytest.mark.parametrize("data_store", ["expected_curie.json"])
 async def test_curie_get(temporary_data_storage: Union[str, Path], test_annotator: sanic.Sanic, data_store: Dict):
     """
@@ -250,7 +250,7 @@ async def test_curie_get(temporary_data_storage: Union[str, Path], test_annotato
 
 
 @pytest.mark.unit
-@pytest.mark.asyncio(scope="module")
+@pytest.mark.asyncio(loop_scope="module")
 @pytest.mark.parametrize(
     "endpoint, batch_curie",
     (
@@ -311,7 +311,7 @@ async def test_curie_post(test_annotator: sanic.Sanic, endpoint: str, batch_curi
 
 
 @pytest.mark.unit
-@pytest.mark.asyncio(scope="module")
+@pytest.mark.asyncio(loop_scope="module")
 @pytest.mark.parametrize("data_store", ["trapi_request.json"])
 async def test_trapi_post(temporary_data_storage: Union[str, Path], test_annotator: sanic.Sanic, data_store: Dict):
     """
@@ -370,7 +370,7 @@ async def test_trapi_post(temporary_data_storage: Union[str, Path], test_annotat
 
 
 @pytest.mark.unit
-@pytest.mark.asyncio(scope="module")
+@pytest.mark.asyncio(loop_scope="module")
 @pytest.mark.parametrize("data_store", ["expected_curie.json"])
 async def test_annotator_get_redirect(
     temporary_data_storage: Union[str, Path], test_annotator: sanic.Sanic, data_store: Dict
@@ -419,7 +419,7 @@ async def test_annotator_get_redirect(
 
 
 @pytest.mark.unit
-@pytest.mark.asyncio(scope="module")
+@pytest.mark.asyncio(loop_scope="module")
 @pytest.mark.parametrize("data_store", ["trapi_request.json"])
 async def test_annotator_post_redirect(
     temporary_data_storage: Union[str, Path], test_annotator: sanic.Sanic, data_store: Dict

tests/test_metadata.py

@@ -8,7 +8,7 @@
 
 
 @pytest.mark.unit
-@pytest.mark.asyncio(scope="module")
+@pytest.mark.asyncio(loop_scope="module")
 async def test_metadata_generation(test_annotator: sanic.Sanic):
     """
     Tests the metadata endpoint for generating the openapi spec

tests/test_query.py

@@ -37,31 +37,6 @@ def test_annotation_client(node_type: str):
             utils.get_client(node_type, SERVICE_PROVIDER_API_HOST)
 
 
-@pytest.mark.unit
-@pytest.mark.asyncio(scope="module")
-@pytest.mark.parametrize("curie_prefix", list(BIOLINK_PREFIX_to_BioThings.keys()))
-async def test_biothings_query(curie_prefix: str):
-    random_index = random.randint(0, 10000)
-    curie_query = f"{curie_prefix}:{str(random_index)}"
-
-    node_type, node_id = utils.parse_curie(curie=curie_query, return_type=True, return_id=True)
-
-    domain_fields = ANNOTATOR_CLIENTS[node_type]["fields"]
-    client = utils.get_client(node_type, SERVICE_PROVIDER_API_HOST)
-    if not client:
-        logger.warning("Failed to get the biothings client for %s type. This type is skipped.", node_type)
-        return {}
-
-    fields = ANNOTATOR_CLIENTS[node_type]["fields"]
-    scopes = ANNOTATOR_CLIENTS[node_type]["scopes"]
-    querymany_result = await client.querymany([node_id], scopes=scopes, fields=fields)
-    logger.info("Done. %s annotation objects returned.", len(querymany_result))
-    query_response = utils.group_by_subfield(collection=querymany_result, search_key="query")
-
-    assert isinstance(query_response, dict)
-    logger.info((f"Query Response: {query_response}" f"Query Fields: {domain_fields}"))
-
-
 @pytest.mark.unit
 @pytest.mark.parametrize(
     "search_keyword, collection, histogram",
@@ -130,3 +105,27 @@ def test_query_post_processing(search_keyword: str, collection: List[Dict], hist
     histogram_response = utils.group_by_subfield(collection=collection, search_key=search_keyword)
     assert isinstance(histogram_response, dict)
     assert histogram_response == histogram
+
+
+@pytest.mark.asyncio(loop_scope="module")
+@pytest.mark.parametrize("curie_prefix", list(BIOLINK_PREFIX_to_BioThings.keys()))
+async def test_biothings_query(curie_prefix: str):
+    random_index = random.randint(0, 10000)
+    curie_query = f"{curie_prefix}:{str(random_index)}"
+
+    node_type, node_id = utils.parse_curie(curie=curie_query, return_type=True, return_id=True)
+
+    domain_fields = ANNOTATOR_CLIENTS[node_type]["fields"]
+    client = utils.get_client(node_type, SERVICE_PROVIDER_API_HOST)
+    if not client:
+        logger.warning("Failed to get the biothings client for %s type. This type is skipped.", node_type)
+        return {}
+
+    fields = ANNOTATOR_CLIENTS[node_type]["fields"]
+    scopes = ANNOTATOR_CLIENTS[node_type]["scopes"]
+    querymany_result = await client.querymany([node_id], scopes=scopes, fields=fields)
+    logger.info("Done. %s annotation objects returned.", len(querymany_result))
+    query_response = utils.group_by_subfield(collection=querymany_result, search_key="query")
+
+    assert isinstance(query_response, dict)
+    logger.info((f"Query Response: {query_response}" f"Query Fields: {domain_fields}"))

tests/test_transformer.py

@@ -16,8 +16,7 @@
 logger.setLevel(logging.DEBUG)
 
 
-@pytest.mark.unit
-@pytest.mark.asyncio(scope="module")
+@pytest.mark.asyncio(loop_scope="module")
 @pytest.mark.parametrize("curie_prefix", list(BIOLINK_PREFIX_to_BioThings.keys()))
 async def test_annotation_transform(curie_prefix: str):
     annotation_instance = Annotator()