From 2ffe82531b61a1c1ea6fab71dc87904db60a3e60 Mon Sep 17 00:00:00 2001 From: Sai Shanmukha Date: Tue, 5 Aug 2025 12:44:36 -0500 Subject: [PATCH 01/14] Move poetry install from common_setup and run it before _setup_db --- bin/_common_setup.sh | 4 ---- bin/test.sh | 6 ++++++ 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/bin/_common_setup.sh b/bin/_common_setup.sh index feff0bd..70d4d4b 100644 --- a/bin/_common_setup.sh +++ b/bin/_common_setup.sh @@ -15,7 +15,3 @@ else fi # Source the environment variables from the metrics setup script source "${CURRENT_DIR}/setup_prometheus.sh" $PROMETHEUS_MULTIPROC_DIR - -echo "installing dependencies with 'poetry install -vv'..." -poetry install -vv -poetry env info diff --git a/bin/test.sh b/bin/test.sh index 02bdd0d..42bba89 100755 --- a/bin/test.sh +++ b/bin/test.sh @@ -4,7 +4,13 @@ set -e CURRENT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)" source "${CURRENT_DIR}/_common_setup.sh" + +echo "installing dependencies with 'poetry install -vv'..." +poetry install -vv +poetry env info + source "${CURRENT_DIR}/_setup_db.sh" + echo "running tests with 'pytest'..." poetry run pytest -vv --cov=gen3workflow --cov=migrations/versions --cov-report term-missing:skip-covered --cov-report xml From 8457295e3917c689f700c0d524fcdd4e72ec3a34 Mon Sep 17 00:00:00 2001 From: Sai Shanmukha Date: Tue, 5 Aug 2025 13:05:32 -0500 Subject: [PATCH 02/14] Test hitting metrics endpoint without s3_root_router --- gen3workflow/app.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gen3workflow/app.py b/gen3workflow/app.py index 1d58e68..c9db95b 100644 --- a/gen3workflow/app.py +++ b/gen3workflow/app.py @@ -68,7 +68,7 @@ async def get_status(): app.include_router(s3_router, tags=["S3"]) app.include_router(storage_router, tags=["Storage"]) app.include_router(system_router, tags=["System"]) - app.include_router(s3_root_router, tags=["S3"]) + # app.include_router(s3_root_router, tags=["S3"]) # Following will update logger level, propagate, and handlers get_logger("gen3workflow", log_level=log_level) From bddf29a50eb4a106877325b87cfc5bb427a4e238 Mon Sep 17 00:00:00 2001 From: Sai Shanmukha Date: Tue, 5 Aug 2025 13:32:09 -0500 Subject: [PATCH 03/14] Place '/metrics' able 's3_root_router' --- gen3workflow/app.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gen3workflow/app.py b/gen3workflow/app.py index c9db95b..0409536 100644 --- a/gen3workflow/app.py +++ b/gen3workflow/app.py @@ -68,7 +68,6 @@ async def get_status(): app.include_router(s3_router, tags=["S3"]) app.include_router(storage_router, tags=["Storage"]) app.include_router(system_router, tags=["System"]) - # app.include_router(s3_root_router, tags=["S3"]) # Following will update logger level, propagate, and handlers get_logger("gen3workflow", log_level=log_level) @@ -99,6 +98,8 @@ async def get_status(): if app.metrics.enabled: app.mount("/metrics", app.metrics.get_asgi_app()) + app.include_router(s3_root_router, tags=["S3"]) + @app.middleware("http") async def middleware_log_response_and_api_metric( request: Request, call_next From cbd68711aa6091d2d448aaff8bf7a567c60aecb7 Mon Sep 17 00:00:00 2001 From: Sai Shanmukha Date: Tue, 5 Aug 2025 14:43:52 -0500 Subject: [PATCH 04/14] Change '/metrics' path --- gen3workflow/app.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gen3workflow/app.py b/gen3workflow/app.py index 0409536..b5adec7 100644 --- a/gen3workflow/app.py +++ b/gen3workflow/app.py @@ -96,7 +96,7 @@ async def get_status(): ) if app.metrics.enabled: - app.mount("/metrics", app.metrics.get_asgi_app()) + app.mount("/metrics/", app.metrics.get_asgi_app()) app.include_router(s3_root_router, tags=["S3"]) From 5c5666dbf1179d6c1021483bd175d9f09f3f97e6 Mon Sep 17 00:00:00 2001 From: Sai Shanmukha Date: Tue, 5 Aug 2025 14:56:58 -0500 Subject: [PATCH 05/14] Add a re-direct from /metrics to /metrics/ for grafana scraping --- gen3workflow/app.py | 2 +- gen3workflow/routes/system.py | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/gen3workflow/app.py b/gen3workflow/app.py index b5adec7..0409536 100644 --- a/gen3workflow/app.py +++ b/gen3workflow/app.py @@ -96,7 +96,7 @@ async def get_status(): ) if app.metrics.enabled: - app.mount("/metrics/", app.metrics.get_asgi_app()) + app.mount("/metrics", app.metrics.get_asgi_app()) app.include_router(s3_root_router, tags=["S3"]) diff --git a/gen3workflow/routes/system.py b/gen3workflow/routes/system.py index 917da5c..dd23791 100644 --- a/gen3workflow/routes/system.py +++ b/gen3workflow/routes/system.py @@ -1,4 +1,5 @@ from fastapi import APIRouter, HTTPException, Request +from fastapi.responses import RedirectResponse from starlette.status import HTTP_500_INTERNAL_SERVER_ERROR from gen3workflow import logger @@ -24,3 +25,8 @@ async def get_status(request: Request) -> dict: except Exception: raise HTTPException(HTTP_500_INTERNAL_SERVER_ERROR, "Unable to reach TES API") return dict(status="OK") + + +@router.get("/metrics", include_in_schema=False) +async def redirect_metrics(): + return RedirectResponse(url="/metrics/") From 6aee2ca5e013b6766bff162b072aaa47a87a7781 Mon Sep 17 00:00:00 2001 From: Sai Shanmukha Date: Tue, 5 Aug 2025 16:12:04 -0500 Subject: [PATCH 06/14] Remove poetry install from `test.sh` --- bin/test.sh | 5 ----- 1 file changed, 5 deletions(-) diff --git a/bin/test.sh b/bin/test.sh index 42bba89..0ffeee9 100755 --- a/bin/test.sh +++ b/bin/test.sh @@ -4,11 +4,6 @@ set -e CURRENT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)" source "${CURRENT_DIR}/_common_setup.sh" - -echo "installing dependencies with 'poetry install -vv'..." -poetry install -vv -poetry env info - source "${CURRENT_DIR}/_setup_db.sh" From 2955d7871d32800b90eba0daa837f06514709bac Mon Sep 17 00:00:00 2001 From: Sai Shanmukha Date: Tue, 5 Aug 2025 16:14:19 -0500 Subject: [PATCH 07/14] Remove empty line --- bin/test.sh | 1 - 1 file changed, 1 deletion(-) diff --git a/bin/test.sh b/bin/test.sh index 0ffeee9..02bdd0d 100755 --- a/bin/test.sh +++ b/bin/test.sh @@ -6,6 +6,5 @@ CURRENT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)" source "${CURRENT_DIR}/_common_setup.sh" source "${CURRENT_DIR}/_setup_db.sh" - echo "running tests with 'pytest'..." poetry run pytest -vv --cov=gen3workflow --cov=migrations/versions --cov-report term-missing:skip-covered --cov-report xml From e254db1dd26cede6decf1fe2ea086aeed17a9830 Mon Sep 17 00:00:00 2001 From: Sai Shanmukha Date: Wed, 6 Aug 2025 12:30:49 -0500 Subject: [PATCH 08/14] Improve unit test to catch if metrics endpoint is missed --- gen3workflow/routes/system.py | 6 +++--- tests/test-gen3workflow-config.yaml | 1 + tests/test_metrics.py | 13 +++++++++++++ 3 files changed, 17 insertions(+), 3 deletions(-) diff --git a/gen3workflow/routes/system.py b/gen3workflow/routes/system.py index dd23791..8c1bbe5 100644 --- a/gen3workflow/routes/system.py +++ b/gen3workflow/routes/system.py @@ -27,6 +27,6 @@ async def get_status(request: Request) -> dict: return dict(status="OK") -@router.get("/metrics", include_in_schema=False) -async def redirect_metrics(): - return RedirectResponse(url="/metrics/") +# @router.get("/metrics", include_in_schema=False) +# async def redirect_metrics(): +# return RedirectResponse(url="/metrics/") diff --git a/tests/test-gen3workflow-config.yaml b/tests/test-gen3workflow-config.yaml index f67d2b8..0f6e3cb 100644 --- a/tests/test-gen3workflow-config.yaml +++ b/tests/test-gen3workflow-config.yaml @@ -4,6 +4,7 @@ ARBORIST_URL: http://test-arborist-server S3_ENDPOINTS_AWS_ACCESS_KEY_ID: test-aws-key-id S3_ENDPOINTS_AWS_SECRET_ACCESS_KEY: test-aws-key +ENABLE_PROMETHEUS_METRICS: true TES_SERVER_URL: http://external-tes-server/tes TASK_IMAGE_WHITELIST: - public.ecr.aws/random/approved/public:* diff --git a/tests/test_metrics.py b/tests/test_metrics.py index c5a8dbd..56d40c9 100644 --- a/tests/test_metrics.py +++ b/tests/test_metrics.py @@ -1,5 +1,6 @@ import pytest from unittest.mock import patch +from conftest import trailing_slash, TEST_USER_TOKEN @pytest.mark.asyncio @@ -19,3 +20,15 @@ async def test_metrics_collection(client, endpoint): else: await client.get(endpoint) mock_metrics.assert_not_called() + + +@pytest.mark.asyncio +async def test_metrics_endpoint(client, trailing_slash): + res = await client.get( + f"/metrics{'/' if trailing_slash else ''}", + headers={"Authorization": f"bearer {TEST_USER_TOKEN}"}, + ) + + # Metrics endpoint is mounted at /metrics/, + # so when trying to access it without a trailing slash, it should redirect, returning a 307 status code. + assert res.status_code == 200 if trailing_slash else 307 From 96186efb7c2f30d8e2ea223c8aac0f45d00279dc Mon Sep 17 00:00:00 2001 From: Sai Shanmukha Date: Sun, 10 Aug 2025 16:45:57 -0500 Subject: [PATCH 09/14] Add redirect `/metrics` to `/metrics/` --- gen3workflow/routes/system.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gen3workflow/routes/system.py b/gen3workflow/routes/system.py index 8c1bbe5..dd23791 100644 --- a/gen3workflow/routes/system.py +++ b/gen3workflow/routes/system.py @@ -27,6 +27,6 @@ async def get_status(request: Request) -> dict: return dict(status="OK") -# @router.get("/metrics", include_in_schema=False) -# async def redirect_metrics(): -# return RedirectResponse(url="/metrics/") +@router.get("/metrics", include_in_schema=False) +async def redirect_metrics(): + return RedirectResponse(url="/metrics/") From c85f89204309d5c1fbaec9881722fb893954fc94 Mon Sep 17 00:00:00 2001 From: Sai Shanmukha Date: Sun, 10 Aug 2025 16:47:23 -0500 Subject: [PATCH 10/14] Update cdispythonutils dependency --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index c0c8a5c..7ed18e1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,7 +25,7 @@ httpx = "<1" jsonschema = "<5" sqlalchemy = { extras = ["asyncio"], version = "<3" } uvicorn = "<1" -cdispyutils = "^2.4.0" +cdispyutils = { git = "https://github.com/uc-cdis/cdis-python-utils.git", branch = "update_registry_in_constructors" } [tool.poetry.group.dev.dependencies] freezegun = "<2" From f1fbc5db6e39776f3d865cb0bed488f9733bdc31 Mon Sep 17 00:00:00 2001 From: Sai Shanmukha Date: Sun, 10 Aug 2025 16:50:30 -0500 Subject: [PATCH 11/14] update poetry lock --- poetry.lock | 1337 +++++++++++++++++++++++++++------------------------ 1 file changed, 708 insertions(+), 629 deletions(-) diff --git a/poetry.lock b/poetry.lock index 13169cb..f04237e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,18 +2,19 @@ [[package]] name = "alembic" -version = "1.15.2" +version = "1.16.4" description = "A database migration tool for SQLAlchemy." optional = false python-versions = ">=3.9" files = [ - {file = "alembic-1.15.2-py3-none-any.whl", hash = "sha256:2e76bd916d547f6900ec4bb5a90aeac1485d2c92536923d0b138c02b126edc53"}, - {file = "alembic-1.15.2.tar.gz", hash = "sha256:1c72391bbdeffccfe317eefba686cb9a3c078005478885413b95c3b26c57a8a7"}, + {file = "alembic-1.16.4-py3-none-any.whl", hash = "sha256:b05e51e8e82efc1abd14ba2af6392897e145930c3e0a2faf2b0da2f7f7fd660d"}, + {file = "alembic-1.16.4.tar.gz", hash = "sha256:efab6ada0dd0fae2c92060800e0bf5c1dc26af15a10e02fb4babff164b4725e2"}, ] [package.dependencies] Mako = "*" SQLAlchemy = ">=1.4.0" +tomli = {version = "*", markers = "python_version < \"3.11\""} typing-extensions = ">=4.12" [package.extras] @@ -32,13 +33,13 @@ files = [ [[package]] name = "anyio" -version = "4.9.0" -description = "High level compatibility layer for multiple asynchronous event loop implementations" +version = "4.10.0" +description = "High-level concurrency and networking framework on top of asyncio or Trio" optional = false python-versions = ">=3.9" files = [ - {file = "anyio-4.9.0-py3-none-any.whl", hash = "sha256:9f76d541cad6e36af7beb62e978876f3b41e3e04f2c1fbf0884604c0a9c4d93c"}, - {file = "anyio-4.9.0.tar.gz", hash = "sha256:673c0c244e15788651a4ff38710fea9675823028a6f08a5eda409e0c9840a028"}, + {file = "anyio-4.10.0-py3-none-any.whl", hash = "sha256:60e474ac86736bbfd6f210f7a61218939c318f43f9972497381f1c5e930ed3d1"}, + {file = "anyio-4.10.0.tar.gz", hash = "sha256:3f3fae35c96039744587aa5b8371e7e8e603c0702999535961dd336026973ba6"}, ] [package.dependencies] @@ -48,8 +49,6 @@ sniffio = ">=1.1" typing_extensions = {version = ">=4.5", markers = "python_version < \"3.13\""} [package.extras] -doc = ["Sphinx (>=8.2,<9.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx_rtd_theme"] -test = ["anyio[trio]", "blockbuster (>=1.5.23)", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "trustme", "truststore (>=0.9.1)", "uvloop (>=0.21)"] trio = ["trio (>=0.26.1)"] [[package]] @@ -150,13 +149,13 @@ tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"] [[package]] name = "authlib" -version = "1.5.2" +version = "1.6.1" description = "The ultimate Python library in building OAuth and OpenID Connect servers and clients." optional = false python-versions = ">=3.9" files = [ - 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connection pooling, file post, and more." optional = false python-versions = ">=3.9" files = [ - {file = "urllib3-2.4.0-py3-none-any.whl", hash = "sha256:4e16665048960a0900c702d4a66415956a584919c03361cac9f1df5c5dd7e813"}, - {file = "urllib3-2.4.0.tar.gz", hash = "sha256:414bc6535b787febd7567804cc015fee39daab8ad86268f1310a9250697de466"}, + {file = "urllib3-2.5.0-py3-none-any.whl", hash = "sha256:e6b01673c0fa6a13e374b50871808eb3bf7046c4b125b216f6bf1cc604cff0dc"}, + {file = "urllib3-2.5.0.tar.gz", hash = "sha256:3fc47733c7e419d4bc3f6b3dc2b4f890bb743906a30d56ba4a5bfa4bbff92760"}, ] [package.extras] @@ -1926,13 +2005,13 @@ zstd = ["zstandard (>=0.18.0)"] [[package]] name = "uvicorn" -version = "0.34.1" +version = "0.35.0" description = "The lightning-fast ASGI server." optional = false python-versions = ">=3.9" files = [ - {file = "uvicorn-0.34.1-py3-none-any.whl", hash = "sha256:984c3a8c7ca18ebaad15995ee7401179212c59521e67bfc390c07fa2b8d2e065"}, - {file = "uvicorn-0.34.1.tar.gz", hash = "sha256:af981725fc4b7ffc5cb3b0e9eda6258a90c4b52cb2a83ce567ae0a7ae1757afc"}, + {file = "uvicorn-0.35.0-py3-none-any.whl", hash = "sha256:197535216b25ff9b785e29a0b79199f55222193d47f820816e7da751e9bc8d4a"}, + {file = "uvicorn-0.35.0.tar.gz", hash = "sha256:bc662f087f7cf2ce11a1d7fd70b90c9f98ef2e2831556dd078d131b96cc94a01"}, ] [package.dependencies] @@ -1941,7 +2020,7 @@ h11 = ">=0.8" typing-extensions = {version = ">=4.0", markers = "python_version < \"3.11\""} [package.extras] -standard = ["colorama (>=0.4)", "httptools (>=0.6.3)", "python-dotenv (>=0.13)", "pyyaml (>=5.1)", "uvloop (>=0.14.0,!=0.15.0,!=0.15.1)", "watchfiles (>=0.13)", "websockets (>=10.4)"] +standard = ["colorama (>=0.4)", "httptools (>=0.6.3)", "python-dotenv (>=0.13)", "pyyaml (>=5.1)", "uvloop (>=0.15.1)", "watchfiles (>=0.13)", "websockets (>=10.4)"] [[package]] name = "werkzeug" @@ -1973,13 +2052,13 @@ files = [ [[package]] name = "zipp" -version = "3.21.0" +version = "3.23.0" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false python-versions = ">=3.9" files = [ - {file = "zipp-3.21.0-py3-none-any.whl", hash = "sha256:ac1bbe05fd2991f160ebce24ffbac5f6d11d83dc90891255885223d42b3cd931"}, - {file = "zipp-3.21.0.tar.gz", hash = "sha256:2c9958f6430a2040341a52eb608ed6dd93ef4392e02ffe219417c1b28b5dd1f4"}, + {file = "zipp-3.23.0-py3-none-any.whl", hash = "sha256:071652d6115ed432f5ce1d34c336c0adfd6a884660d1e9712a256d3d3bd4b14e"}, + {file = "zipp-3.23.0.tar.gz", hash = "sha256:a07157588a12518c9d4034df3fbbee09c814741a33ff63c05fa29d26a2404166"}, ] [package.extras] @@ -1987,10 +2066,10 @@ check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] enabler = ["pytest-enabler (>=2.2)"] -test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more_itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<4" -content-hash = "59de96f38f98da43f9cc316ca6f1a6205681093075e5f2dca46197ff37fc3def" +content-hash = "664679309a564856a158a731365a5315382c20d3b1b6396ac0931fc2748d77c4" From 3f6416c8ea6ca77444aedc329cc7d5af9c7efdc2 Mon Sep 17 00:00:00 2001 From: Sai Shanmukha Date: Sun, 10 Aug 2025 17:22:25 -0500 Subject: [PATCH 12/14] Support metrics for both with and without trailing slash --- gen3workflow/app.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gen3workflow/app.py b/gen3workflow/app.py index 0409536..76b888f 100644 --- a/gen3workflow/app.py +++ b/gen3workflow/app.py @@ -122,7 +122,7 @@ async def middleware_log_response_and_api_metric( # NOTE: If adding more endpoints to metrics, try making it configurable using a list of paths and methods in config. # For now, we are only interested in the "/ga4gh/tes/v1/tasks" endpoint for metrics. - if method != "POST" or path != "/ga4gh/tes/v1/tasks": + if method != "POST" or path.rstrip("/") != "/ga4gh/tes/v1/tasks": return response metrics = app.metrics From 34c1a7b3456420e4acdde5d234cf497c8de0c4c6 Mon Sep 17 00:00:00 2001 From: Sai Shanmukha Date: Mon, 11 Aug 2025 09:04:58 -0500 Subject: [PATCH 13/14] Update next_url for redirect --- tests/test_metrics.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/tests/test_metrics.py b/tests/test_metrics.py index 56d40c9..0a57fd1 100644 --- a/tests/test_metrics.py +++ b/tests/test_metrics.py @@ -31,4 +31,8 @@ async def test_metrics_endpoint(client, trailing_slash): # Metrics endpoint is mounted at /metrics/, # so when trying to access it without a trailing slash, it should redirect, returning a 307 status code. - assert res.status_code == 200 if trailing_slash else 307 + if trailing_slash: + assert res.status_code == 200 + else: + assert res.status_code == 307 + assert res.next_request.url == "http://test-gen3-wf/metrics/" From cb067d9422d25434bef301a940c4e409c69b32fa Mon Sep 17 00:00:00 2001 From: Sai Shanmukha Date: Fri, 15 Aug 2025 13:25:21 -0500 Subject: [PATCH 14/14] Reverting changes related to PR #89 --- gen3workflow/app.py | 5 +- gen3workflow/routes/system.py | 6 - poetry.lock | 1337 +++++++++++++-------------- pyproject.toml | 2 +- tests/test-gen3workflow-config.yaml | 1 - tests/test_metrics.py | 17 - 6 files changed, 632 insertions(+), 736 deletions(-) diff --git a/gen3workflow/app.py b/gen3workflow/app.py index 76b888f..1d58e68 100644 --- a/gen3workflow/app.py +++ b/gen3workflow/app.py @@ -68,6 +68,7 @@ async def get_status(): app.include_router(s3_router, tags=["S3"]) app.include_router(storage_router, tags=["Storage"]) app.include_router(system_router, tags=["System"]) + app.include_router(s3_root_router, tags=["S3"]) # Following will update logger level, propagate, and handlers get_logger("gen3workflow", log_level=log_level) @@ -98,8 +99,6 @@ async def get_status(): if app.metrics.enabled: app.mount("/metrics", app.metrics.get_asgi_app()) - app.include_router(s3_root_router, tags=["S3"]) - @app.middleware("http") async def middleware_log_response_and_api_metric( request: Request, call_next @@ -122,7 +121,7 @@ async def middleware_log_response_and_api_metric( # NOTE: If adding more endpoints to metrics, try making it configurable using a list of paths and methods in config. # For now, we are only interested in the "/ga4gh/tes/v1/tasks" endpoint for metrics. - if method != "POST" or path.rstrip("/") != "/ga4gh/tes/v1/tasks": + if method != "POST" or path != "/ga4gh/tes/v1/tasks": return response metrics = app.metrics diff --git a/gen3workflow/routes/system.py b/gen3workflow/routes/system.py index dd23791..917da5c 100644 --- a/gen3workflow/routes/system.py +++ b/gen3workflow/routes/system.py @@ -1,5 +1,4 @@ from fastapi import APIRouter, HTTPException, Request -from fastapi.responses import RedirectResponse from starlette.status import HTTP_500_INTERNAL_SERVER_ERROR from gen3workflow import logger @@ -25,8 +24,3 @@ async def get_status(request: Request) -> dict: except Exception: raise HTTPException(HTTP_500_INTERNAL_SERVER_ERROR, "Unable to reach TES API") return dict(status="OK") - - -@router.get("/metrics", include_in_schema=False) -async def redirect_metrics(): - return RedirectResponse(url="/metrics/") diff --git a/poetry.lock b/poetry.lock index f04237e..13169cb 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,19 +2,18 @@ [[package]] name = "alembic" -version = "1.16.4" +version = "1.15.2" description = "A database migration tool for SQLAlchemy." optional = false python-versions = ">=3.9" files = [ - {file = "alembic-1.16.4-py3-none-any.whl", hash = "sha256:b05e51e8e82efc1abd14ba2af6392897e145930c3e0a2faf2b0da2f7f7fd660d"}, - {file = "alembic-1.16.4.tar.gz", hash = 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Python library in building OAuth and OpenID Connect servers and clients." optional = false python-versions = ">=3.9" files = [ - {file = "authlib-1.6.1-py2.py3-none-any.whl", hash = "sha256:e9d2031c34c6309373ab845afc24168fe9e93dc52d252631f52642f21f5ed06e"}, - {file = "authlib-1.6.1.tar.gz", hash = "sha256:4dffdbb1460ba6ec8c17981a4c67af7d8af131231b5a36a88a1e8c80c111cdfd"}, + {file = "authlib-1.5.2-py2.py3-none-any.whl", hash = "sha256:8804dd4402ac5e4a0435ac49e0b6e19e395357cfa632a3f624dcb4f6df13b4b1"}, + {file = "authlib-1.5.2.tar.gz", hash = "sha256:fe85ec7e50c5f86f1e2603518bb3b4f632985eb4a355e52256530790e326c512"}, ] [package.dependencies] @@ -209,32 +210,32 @@ files = [ [[package]] name = "boto3" -version = "1.40.6" +version = "1.37.34" description = "The AWS SDK for Python" optional = false -python-versions = ">=3.9" +python-versions = ">=3.8" files = [ - {file = "boto3-1.40.6-py3-none-any.whl", hash = "sha256:7685085b8ea679dd858330834c16364c61c5830edb892c5864fb12ed68798708"}, - 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connection pooling, file post, and more." optional = false python-versions = ">=3.9" files = [ - {file = "urllib3-2.5.0-py3-none-any.whl", hash = "sha256:e6b01673c0fa6a13e374b50871808eb3bf7046c4b125b216f6bf1cc604cff0dc"}, - {file = "urllib3-2.5.0.tar.gz", hash = "sha256:3fc47733c7e419d4bc3f6b3dc2b4f890bb743906a30d56ba4a5bfa4bbff92760"}, + {file = "urllib3-2.4.0-py3-none-any.whl", hash = "sha256:4e16665048960a0900c702d4a66415956a584919c03361cac9f1df5c5dd7e813"}, + {file = "urllib3-2.4.0.tar.gz", hash = "sha256:414bc6535b787febd7567804cc015fee39daab8ad86268f1310a9250697de466"}, ] [package.extras] @@ -2005,13 +1926,13 @@ zstd = ["zstandard (>=0.18.0)"] [[package]] name = "uvicorn" -version = "0.35.0" +version = "0.34.1" description = "The lightning-fast ASGI server." optional = false python-versions = ">=3.9" files = [ - {file = "uvicorn-0.35.0-py3-none-any.whl", hash = "sha256:197535216b25ff9b785e29a0b79199f55222193d47f820816e7da751e9bc8d4a"}, - {file = "uvicorn-0.35.0.tar.gz", hash = "sha256:bc662f087f7cf2ce11a1d7fd70b90c9f98ef2e2831556dd078d131b96cc94a01"}, + {file = "uvicorn-0.34.1-py3-none-any.whl", hash = "sha256:984c3a8c7ca18ebaad15995ee7401179212c59521e67bfc390c07fa2b8d2e065"}, + {file = "uvicorn-0.34.1.tar.gz", hash = "sha256:af981725fc4b7ffc5cb3b0e9eda6258a90c4b52cb2a83ce567ae0a7ae1757afc"}, ] [package.dependencies] @@ -2020,7 +1941,7 @@ h11 = ">=0.8" typing-extensions = {version = ">=4.0", markers = "python_version < \"3.11\""} [package.extras] -standard = ["colorama (>=0.4)", "httptools (>=0.6.3)", "python-dotenv (>=0.13)", "pyyaml (>=5.1)", "uvloop (>=0.15.1)", "watchfiles (>=0.13)", "websockets (>=10.4)"] +standard = ["colorama (>=0.4)", "httptools (>=0.6.3)", "python-dotenv (>=0.13)", "pyyaml (>=5.1)", "uvloop (>=0.14.0,!=0.15.0,!=0.15.1)", "watchfiles (>=0.13)", "websockets (>=10.4)"] [[package]] name = "werkzeug" @@ -2052,13 +1973,13 @@ files = [ [[package]] name = "zipp" -version = "3.23.0" +version = "3.21.0" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false python-versions = ">=3.9" files = [ - {file = "zipp-3.23.0-py3-none-any.whl", hash = "sha256:071652d6115ed432f5ce1d34c336c0adfd6a884660d1e9712a256d3d3bd4b14e"}, - {file = "zipp-3.23.0.tar.gz", hash = "sha256:a07157588a12518c9d4034df3fbbee09c814741a33ff63c05fa29d26a2404166"}, + {file = "zipp-3.21.0-py3-none-any.whl", hash = "sha256:ac1bbe05fd2991f160ebce24ffbac5f6d11d83dc90891255885223d42b3cd931"}, + {file = "zipp-3.21.0.tar.gz", hash = "sha256:2c9958f6430a2040341a52eb608ed6dd93ef4392e02ffe219417c1b28b5dd1f4"}, ] [package.extras] @@ -2066,10 +1987,10 @@ check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] enabler = ["pytest-enabler (>=2.2)"] -test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more_itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<4" -content-hash = "664679309a564856a158a731365a5315382c20d3b1b6396ac0931fc2748d77c4" +content-hash = "59de96f38f98da43f9cc316ca6f1a6205681093075e5f2dca46197ff37fc3def" diff --git a/pyproject.toml b/pyproject.toml index 7ed18e1..c0c8a5c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,7 +25,7 @@ httpx = "<1" jsonschema = "<5" sqlalchemy = { extras = ["asyncio"], version = "<3" } uvicorn = "<1" -cdispyutils = { git = "https://github.com/uc-cdis/cdis-python-utils.git", branch = "update_registry_in_constructors" } +cdispyutils = "^2.4.0" [tool.poetry.group.dev.dependencies] freezegun = "<2" diff --git a/tests/test-gen3workflow-config.yaml b/tests/test-gen3workflow-config.yaml index 0f6e3cb..f67d2b8 100644 --- a/tests/test-gen3workflow-config.yaml +++ b/tests/test-gen3workflow-config.yaml @@ -4,7 +4,6 @@ ARBORIST_URL: http://test-arborist-server S3_ENDPOINTS_AWS_ACCESS_KEY_ID: test-aws-key-id S3_ENDPOINTS_AWS_SECRET_ACCESS_KEY: test-aws-key -ENABLE_PROMETHEUS_METRICS: true TES_SERVER_URL: http://external-tes-server/tes TASK_IMAGE_WHITELIST: - public.ecr.aws/random/approved/public:* diff --git a/tests/test_metrics.py b/tests/test_metrics.py index 0a57fd1..c5a8dbd 100644 --- a/tests/test_metrics.py +++ b/tests/test_metrics.py @@ -1,6 +1,5 @@ import pytest from unittest.mock import patch -from conftest import trailing_slash, TEST_USER_TOKEN @pytest.mark.asyncio @@ -20,19 +19,3 @@ async def test_metrics_collection(client, endpoint): else: await client.get(endpoint) mock_metrics.assert_not_called() - - -@pytest.mark.asyncio -async def test_metrics_endpoint(client, trailing_slash): - res = await client.get( - f"/metrics{'/' if trailing_slash else ''}", - headers={"Authorization": f"bearer {TEST_USER_TOKEN}"}, - ) - - # Metrics endpoint is mounted at /metrics/, - # so when trying to access it without a trailing slash, it should redirect, returning a 307 status code. - if trailing_slash: - assert res.status_code == 200 - else: - assert res.status_code == 307 - assert res.next_request.url == "http://test-gen3-wf/metrics/"