diff --git a/src/backend/aspen/api/views/tests/test_auth.py b/src/backend/aspen/api/views/tests/test_auth.py index 612f09ba4..09004b2d9 100644 --- a/src/backend/aspen/api/views/tests/test_auth.py +++ b/src/backend/aspen/api/views/tests/test_auth.py @@ -258,7 +258,7 @@ async def test_callback_syncs_auth0_user_roles( res = await http_client.get( "/v2/auth/callback", - allow_redirects=False, + follow_redirects=False, ) assert res.status_code == 307 assert auth0_apiclient.get_user_orgs.call_count == 1 # type: ignore @@ -285,7 +285,7 @@ async def test_callback_doesnt_sync_localdev_roles( res = await http_client.get( "/v2/auth/callback", - allow_redirects=False, + follow_redirects=False, ) assert res.status_code == 307 assert auth0_apiclient.get_user_orgs.call_count == 0 # type: ignore @@ -315,7 +315,7 @@ async def test_callback_ff_doesnt_sync_auth0_user_roles( res = await http_client.get( "/v2/auth/callback", - allow_redirects=False, + follow_redirects=False, ) assert res.status_code == 307 assert auth0_apiclient.get_user_orgs.call_count == 0 # type: ignore @@ -340,7 +340,7 @@ async def test_callback_error_redirects( ): res = await http_client.get( "/v2/auth/callback", - allow_redirects=False, + follow_redirects=False, params={"error_description": "invitation not found or already used"}, ) assert res.status_code == 307 @@ -349,7 +349,7 @@ async def test_callback_error_redirects( res = await http_client.get( "/v2/auth/callback", - allow_redirects=False, + follow_redirects=False, params={"error_description": "expired"}, ) assert res.status_code == 307 @@ -387,7 +387,7 @@ async def test_redirect_to_samples_if_exists( res = await http_client.get( "/v2/auth/callback", - allow_redirects=False, + follow_redirects=False, ) assert res.status_code == 307 assert auth0_apiclient.get_user_orgs.call_count == 0 # type: ignore @@ -422,7 +422,7 @@ async def test_redirect_to_group_welcome_if_new( res = await http_client.get( "/v2/auth/callback", - allow_redirects=False, + follow_redirects=False, ) assert res.status_code == 307 assert res.is_redirect diff --git a/src/backend/aspen/api/views/tests/test_health.py b/src/backend/aspen/api/views/tests/test_health.py index 17edd533e..c5829ce32 100644 --- a/src/backend/aspen/api/views/tests/test_health.py +++ b/src/backend/aspen/api/views/tests/test_health.py @@ -5,6 +5,6 @@ async def test_healthcheck(http_client: AsyncClient) -> None: - response = await http_client.get("/v2/health") + response = await http_client.get("/v2/health", follow_redirects=True) assert response.status_code == 200 assert response.json() == {"healthy": True} diff --git a/src/backend/aspen/api/views/tests/test_invitation_flows.py b/src/backend/aspen/api/views/tests/test_invitation_flows.py index 03834c2f0..0b04b8b3c 100644 --- a/src/backend/aspen/api/views/tests/test_invitation_flows.py +++ b/src/backend/aspen/api/views/tests/test_invitation_flows.py @@ -102,7 +102,7 @@ async def make_login_request( "/v2/auth/login", params=login_params, headers=auth_headers, - allow_redirects=False, + follow_redirects=False, ) return res @@ -264,7 +264,7 @@ async def test_callback_redirect( res = await http_client.get( "/v2/auth/callback", headers=auth_headers, - allow_redirects=False, + follow_redirects=False, ) assert "process_invitation" in res.headers["Location"] _, _, path, _, query, _ = urlparse(res.headers["Location"]) @@ -306,7 +306,7 @@ async def test_process_invitation_success( "/v2/auth/process_invitation", params=login_params, headers=auth_headers, - allow_redirects=False, + follow_redirects=False, ) auth0_org = {"id": group.auth0_org_id, "display_name": "", "name": ""} auth0_apiclient.add_org_member.assert_called_once_with( # type: ignore @@ -353,7 +353,7 @@ async def test_process_invitation_failures( "/v2/auth/process_invitation", params=login_params, headers=auth_headers, - allow_redirects=False, + follow_redirects=False, ) assert res.status_code == 400 @@ -368,7 +368,7 @@ async def test_process_invitation_failures( "/v2/auth/process_invitation", params=login_params, headers=auth_headers, - allow_redirects=False, + follow_redirects=False, ) assert res.headers["Location"] == "/v2/auth/callback" redirect_kwargs = auth0_oauth.authorize_redirect.call_args.kwargs @@ -386,6 +386,6 @@ async def test_process_invitation_failures( "/v2/auth/process_invitation", params=login_params, headers=auth_headers, - allow_redirects=False, + follow_redirects=False, ) assert res.status_code == 401 diff --git a/src/backend/aspen/api/views/tests/test_samples.py b/src/backend/aspen/api/views/tests/test_samples.py index 3bc83612c..5166b82bf 100644 --- a/src/backend/aspen/api/views/tests/test_samples.py +++ b/src/backend/aspen/api/views/tests/test_samples.py @@ -1113,6 +1113,7 @@ async def test_update_samples_success( f"/v2/orgs/{group_id}/pathogens/{pathogen_slug}/samples", json=request_data, headers=auth_headers, + follow_redirects=True, ) api_response = {row["id"]: row for row in res.json()["samples"]} @@ -1205,6 +1206,7 @@ async def test_update_samples_access_denied( f"/v2/orgs/{group.id}/pathogens/{pathogen.slug}/samples", json=data, headers=auth_headers, + follow_redirects=True, ) assert res.status_code == 404 @@ -1309,6 +1311,7 @@ async def test_update_samples_request_failures( f"/v2/orgs/{group.id}/pathogens/{pathogen.slug}/samples", json=data, headers=auth_headers, + follow_redirects=True, ) assert res.status_code == response_code diff --git a/src/backend/pipeline_tests/test_gisaid_pipeline.py b/src/backend/pipeline_tests/test_gisaid_pipeline.py index bf6718f6e..4b4485979 100644 --- a/src/backend/pipeline_tests/test_gisaid_pipeline.py +++ b/src/backend/pipeline_tests/test_gisaid_pipeline.py @@ -31,7 +31,7 @@ def test_public_repo_db_objects_were_created(session): assert sample.region == "North America" assert sample.country == "USA" assert sample.division == "Texas" - assert sample.location == "" + assert sample.location == None # noqa: E711 # TODO - I have no idea how this ISL is fetched by ncov-ingest assert sample.isl == "EPI_ISL_4630413" diff --git a/src/backend/poetry.lock b/src/backend/poetry.lock index 42e5085c4..78b3f7b62 100644 --- a/src/backend/poetry.lock +++ b/src/backend/poetry.lock @@ -2,14 +2,14 @@ [[package]] name = "alembic" -version = "1.9.2" +version = "1.9.4" description = "A database migration tool for SQLAlchemy." category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "alembic-1.9.2-py3-none-any.whl", hash = "sha256:e8a6ff9f3b1887e1fed68bfb8fb9a000d8f61c21bdcc85b67bb9f87fcbc4fce3"}, - {file = "alembic-1.9.2.tar.gz", hash = "sha256:6880dec4f28dd7bd999d2ed13fbe7c9d4337700a44d11a524c0ce0c59aaf0dbd"}, + {file = "alembic-1.9.4-py3-none-any.whl", hash = "sha256:6f1c2207369bf4f49f952057a33bb017fbe5c148c2a773b46906b806ea6e825f"}, + {file = "alembic-1.9.4.tar.gz", hash = "sha256:4d3bd32ecdbb7bbfb48a9fe9e6d6fd6a831a1b59d03e26e292210237373e7db5"}, ] [package.dependencies] @@ -23,25 +23,26 @@ tz = ["python-dateutil"] [[package]] name = "anyio" -version = "3.6.2" +version = "3.7.1" description = "High level compatibility layer for multiple asynchronous event loop implementations" category = "main" optional = false -python-versions = ">=3.6.2" +python-versions = ">=3.7" files = [ - {file = "anyio-3.6.2-py3-none-any.whl", hash = "sha256:fbbe32bd270d2a2ef3ed1c5d45041250284e31fc0a4df4a5a6071842051a51e3"}, - {file = "anyio-3.6.2.tar.gz", hash = "sha256:25ea0d673ae30af41a0c442f81cf3b38c7e79fdc7b60335a4c14e05eb0947421"}, + {file = "anyio-3.7.1-py3-none-any.whl", hash = "sha256:91dee416e570e92c64041bd18b900d1d6fa78dff7048769ce5ac5ddad004fbb5"}, + {file = "anyio-3.7.1.tar.gz", hash = "sha256:44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780"}, ] [package.dependencies] +exceptiongroup = {version = "*", markers = "python_version < \"3.11\""} idna = ">=2.8" sniffio = ">=1.1" typing-extensions = {version = "*", markers = "python_version < \"3.8\""} [package.extras] -doc = ["packaging", "sphinx-autodoc-typehints 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