diff --git a/Dockerfile b/Dockerfile index 2dfaf54..306d759 100644 --- a/Dockerfile +++ b/Dockerfile @@ -36,4 +36,6 @@ USER gen3 WORKDIR /${appname} -CMD ["poetry", "run", "gunicorn", "gen3workflow.app:app", "-k", "uvicorn.workers.UvicornWorker", "-c", "gunicorn.conf.py"] +RUN chmod 755 bin/run.sh + +CMD ["bash", "bin/run.sh"] diff --git a/bin/_common_setup.sh b/bin/_common_setup.sh index b981b3a..feff0bd 100644 --- a/bin/_common_setup.sh +++ b/bin/_common_setup.sh @@ -6,45 +6,16 @@ set -e CURRENT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)" +if [ -f "/src/gen3-workflow-config.yaml" ]; then + # For multi-worker Gunicorn setups; requires PROMETHEUS_MULTIPROC_DIR to be set before startup, + # here we assume the config file is mounted at /src via cloud-automation. + PROMETHEUS_MULTIPROC_DIR=$(grep 'PROMETHEUS_MULTIPROC_DIR:' /src/gen3-workflow-config.yaml | awk -F': ' '{print $2}' | tr -d '"') +else + PROMETHEUS_MULTIPROC_DIR="" +fi # Source the environment variables from the metrics setup script -# source "${CURRENT_DIR}/setup_prometheus" +source "${CURRENT_DIR}/setup_prometheus.sh" $PROMETHEUS_MULTIPROC_DIR echo "installing dependencies with 'poetry install -vv'..." poetry install -vv poetry env info -echo "ensuring db exists" - -# Get the username, password, host, port, and database name -db_settings=$(poetry run python $CURRENT_DIR/../gen3workflow/config.py | tail -1) -if [ -z "${db_settings}" ]; then - echo "'gen3workflow/config.py' did not return DB settings" - exit 1 -fi -db_settings_array=($db_settings) -HOST=${db_settings_array[0]} -PORT=${db_settings_array[1]} -USER=${db_settings_array[2]} -PASSWORD=${db_settings_array[3]} -DB_NAME=${db_settings_array[4]} - -if [ -z "${HOST}" ] || [ -z "${PORT}" ] || [ -z "${USER}" ] || [ -z "${PASSWORD}" ] || [ -z "${DB_NAME}" ]; then - echo "Failed to extract one or more components from DB settings" - exit 1 -fi - -echo "Extracted database name: ${DB_NAME}" -echo "Extracted username: ${USER}" - -# Check if the database exists -# Use the full connection string to connect directly -if [ "$( PGPASSWORD="${PASSWORD}" psql -h "${HOST}" -p "${PORT}" -U "${USER}" -d postgres -XtAc "SELECT 1 FROM pg_database WHERE datname='${DB_NAME}'" )" = '1' ] -then - echo "Database ${DB_NAME} already exists." -else - echo "Database ${DB_NAME} does not exist. Creating it..." - # Connect to the default postgres database to create the new database - PGPASSWORD="${PASSWORD}" psql -h "${HOST}" -p "${PORT}" -U "${USER}" -d postgres -c "CREATE DATABASE \"${DB_NAME}\";" -fi - -echo "running db migration with 'poetry run alembic upgrade head'..." -poetry run alembic upgrade head diff --git a/bin/_setup_db.sh b/bin/_setup_db.sh new file mode 100644 index 0000000..a848d49 --- /dev/null +++ b/bin/_setup_db.sh @@ -0,0 +1,36 @@ +echo "ensuring db exists" + +# Get the username, password, host, port, and database name +db_settings=$(poetry run python $CURRENT_DIR/../gen3workflow/config.py | tail -1) +if [ -z "${db_settings}" ]; then + echo "'gen3workflow/config.py' did not return DB settings" + exit 1 +fi +db_settings_array=($db_settings) +HOST=${db_settings_array[0]} +PORT=${db_settings_array[1]} +USER=${db_settings_array[2]} +PASSWORD=${db_settings_array[3]} +DB_NAME=${db_settings_array[4]} + +if [ -z "${HOST}" ] || [ -z "${PORT}" ] || [ -z "${USER}" ] || [ -z "${PASSWORD}" ] || [ -z "${DB_NAME}" ]; then + echo "Failed to extract one or more components from DB settings" + exit 1 +fi + +echo "Extracted database name: ${DB_NAME}" +echo "Extracted username: ${USER}" + +# Check if the database exists +# Use the full connection string to connect directly +if [ "$( PGPASSWORD="${PASSWORD}" psql -h "${HOST}" -p "${PORT}" -U "${USER}" -d postgres -XtAc "SELECT 1 FROM pg_database WHERE datname='${DB_NAME}'" )" = '1' ] +then + echo "Database ${DB_NAME} already exists." +else + echo "Database ${DB_NAME} does not exist. Creating it..." + # Connect to the default postgres database to create the new database + PGPASSWORD="${PASSWORD}" psql -h "${HOST}" -p "${PORT}" -U "${USER}" -d postgres -c "CREATE DATABASE \"${DB_NAME}\";" +fi + +echo "running db migration with 'poetry run alembic upgrade head'..." +poetry run alembic upgrade head diff --git a/bin/run.sh b/bin/run.sh new file mode 100755 index 0000000..1be9879 --- /dev/null +++ b/bin/run.sh @@ -0,0 +1,24 @@ +#!/usr/bin/env bash +set -e + +# Mostly simulates the production run of the app as described in the Dockerfile. +# Uses Gunicorn, multiple Uvicorn workers +# Small config overrides for local dev, like hot reload when the code is modified and logs to stdout + +CURRENT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)" +echo $CURRENT_DIR +export ENV="production" + +source "${CURRENT_DIR}/bin/_common_setup.sh" + +#TODO: if we need a DB later, run `source "${CURRENT_DIR}/_setup_db.sh` +#source "${CURRENT_DIR}/_setup_db.sh + + +poetry run gunicorn \ + gen3workflow.app:app \ + -k uvicorn.workers.UvicornWorker \ + -c gunicorn.conf.py \ + --reload \ + --access-logfile - \ + --error-logfile - diff --git a/bin/setup_prometheus.sh b/bin/setup_prometheus.sh new file mode 100755 index 0000000..bc0618a --- /dev/null +++ b/bin/setup_prometheus.sh @@ -0,0 +1,33 @@ +#!/usr/bin/env bash +# Prepares the prometheus_multiproc_dir folder to store the metrics from separate workers (per PID) +# +# This script is called by: +# Dockerfile & run.py +# - So local runs setup necessary environment vars and folders for prometheus metrics +# Test framework in conftest +# - So test runs setup necessary environment vars and folders for prometheus metrics + +# Usage: +# ./setup_prometheus [DIR] [true] + +# Default directory if no argument is provided +DIR=${1:-/var/tmp/prometheus_metrics} + +# Determine whether to wipe the directory (default is to wipe) +SETUP_DIR=${2:-true} + +set -ex + +if [[ "$SETUP_DIR" == "true" ]]; then + echo "setting up $PROMETHEUS_MULTIPROC_DIR. clearing existing files, ensuring it exists, chmod 755" + rm -Rf "$DIR" + mkdir -p "$DIR" + chmod 755 "$DIR" +fi + +if id -u gen3 &>/dev/null; then + chown "$(id -u gen3)":"$(id -g gen3)" "$DIR" +fi + +export PROMETHEUS_MULTIPROC_DIR="$DIR" +echo "PROMETHEUS_MULTIPROC_DIR is $PROMETHEUS_MULTIPROC_DIR" diff --git a/bin/test.sh b/bin/test.sh index ac49b59..4c8e7b7 100755 --- a/bin/test.sh +++ b/bin/test.sh @@ -4,6 +4,7 @@ set -e CURRENT_DIR="$(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 --cov-report term-missing:skip-covered --cov-report xml diff --git a/docs/metrics.md b/docs/metrics.md new file mode 100644 index 0000000..1530e73 --- /dev/null +++ b/docs/metrics.md @@ -0,0 +1,11 @@ +## Metrics + +Metrics can be exposed at a `/metrics` endpoint compatible with Prometheus scraping and visualized in Prometheus or +Graphana, etc. + +The metrics are defined in `gen3workflow/metrics.py` as follows: + +* **gen3_workflow_api_requests_total**: API requests for made to Gen3-Workflow service. +* ** **More metrics yet to be decided** ** + +You can [run Prometheus locally](https://github.com/prometheus/prometheus) if you want to test or visualize these. diff --git a/docs/openapi.yaml b/docs/openapi.yaml index da6fe0b..a6c5b32 100644 --- a/docs/openapi.yaml +++ b/docs/openapi.yaml @@ -47,6 +47,7 @@ paths: content: application/json: schema: + additionalProperties: true title: Response Get Status Get type: object description: Successful Response @@ -61,6 +62,7 @@ paths: content: application/json: schema: + additionalProperties: true title: Response Get Status Status Get type: object description: Successful Response @@ -75,6 +77,7 @@ paths: content: application/json: schema: + additionalProperties: true title: Response Get Version Version Get type: object description: Successful Response @@ -89,6 +92,7 @@ paths: content: application/json: schema: + additionalProperties: true title: Response Service Info Ga4Gh Tes V1 Service Info Get type: object description: Successful Response @@ -105,6 +109,7 @@ paths: content: application/json: schema: + additionalProperties: true title: Response List Tasks Ga4Gh Tes V1 Tasks Get type: object description: Successful Response @@ -120,6 +125,7 @@ paths: content: application/json: schema: + additionalProperties: true title: Response Create Task Ga4Gh Tes V1 Tasks Post type: object description: Successful Response @@ -143,6 +149,7 @@ paths: content: application/json: schema: + additionalProperties: true title: Response Get Task Ga4Gh Tes V1 Tasks Task Id Get type: object description: Successful Response @@ -172,6 +179,7 @@ paths: content: application/json: schema: + additionalProperties: true title: Response Cancel Task Ga4Gh Tes V1 Tasks Task Id Cancel Post type: object description: Successful Response @@ -451,6 +459,7 @@ paths: content: application/json: schema: + additionalProperties: true title: Response Get Storage Info Storage Info Get type: object description: Successful Response diff --git a/gen3workflow/app.py b/gen3workflow/app.py index 936a63a..ce9bc3c 100644 --- a/gen3workflow/app.py +++ b/gen3workflow/app.py @@ -1,17 +1,21 @@ from fastapi import FastAPI +from fastapi.security import HTTPAuthorizationCredentials import httpx from importlib.metadata import version import os +import time from cdislogging import get_logger from gen3authz.client.arborist.async_client import ArboristClient - +from fastapi import Request, HTTPException from gen3workflow import logger from gen3workflow.config import config +from gen3workflow.metrics import Metrics from gen3workflow.routes.ga4gh_tes import router as ga4gh_tes_router from gen3workflow.routes.s3 import router as s3_router from gen3workflow.routes.storage import router as storage_router from gen3workflow.routes.system import router as system_router +from gen3workflow.auth import Auth def get_app(httpx_client=None) -> FastAPI: @@ -54,6 +58,49 @@ def get_app(httpx_client=None) -> FastAPI: logger=get_logger("gen3workflow.gen3authz", log_level=log_level), ) + app.metrics = Metrics( + enabled=config["ENABLE_PROMETHEUS_METRICS"], + prometheus_dir=config["PROMETHEUS_MULTIPROC_DIR"], + ) + + if app.metrics.enabled: + app.mount("/metrics", app.metrics.get_asgi_app()) + + @app.middleware("http") + async def middleware_log_response_and_api_metric( + request: Request, call_next + ) -> None: + """ + This FastAPI middleware effectively allows pre and post logic to a request. + + We are using this to log the response consistently across defined endpoints (including execution time). + + Args: + request (Request): the incoming HTTP request + call_next (Callable): function to call (this is handled by FastAPI's middleware support) + """ + start_time = time.perf_counter() + response = await call_next(request) + response_time_seconds = time.perf_counter() - start_time + + path = request.url.path + method = request.method + + # 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": + return response + + metrics = app.metrics + metrics.add_create_task_api_interaction( + method=method, + path=path, + response_time_seconds=response_time_seconds, + status_code=response.status_code, + ) + + return response + return app diff --git a/gen3workflow/auth.py b/gen3workflow/auth.py index 224c780..b118515 100644 --- a/gen3workflow/auth.py +++ b/gen3workflow/auth.py @@ -1,3 +1,4 @@ +from typing import Union from authutils.token.fastapi import access_token from fastapi import HTTPException, Security from fastapi.security import HTTPAuthorizationCredentials, HTTPBearer @@ -65,6 +66,13 @@ async def get_token_claims(self) -> dict: return token_claims + async def get_user_id(self) -> Union[str, None]: + try: + token_claims = await self.get_token_claims() + except Exception: + return None + return token_claims.get("sub") + async def authorize( self, method: str, diff --git a/gen3workflow/config-default.yaml b/gen3workflow/config-default.yaml index 48e5476..7af2bfd 100644 --- a/gen3workflow/config-default.yaml +++ b/gen3workflow/config-default.yaml @@ -53,3 +53,11 @@ TASK_IMAGE_WHITELIST: [] # - public.ecr.aws/random/approved/public:* # - 9876543210.dkr.ecr.us-east-1.amazonaws.com/approved/{username}:abc # - quay.io/nextflow/bash:* + + +############# +# METRICS # +############# + +ENABLE_PROMETHEUS_METRICS: false +PROMETHEUS_MULTIPROC_DIR: /var/tmp/prometheus_metrics diff --git a/gen3workflow/config.py b/gen3workflow/config.py index d5bb7cc..fde48ca 100644 --- a/gen3workflow/config.py +++ b/gen3workflow/config.py @@ -61,6 +61,8 @@ def validate_top_level_configs(self) -> None: "DB_CONNECTION_STRING": {"type": "string"}, "TASK_IMAGE_WHITELIST": {"type": "array", "items": {"type": "string"}}, "TES_SERVER_URL": {"type": "string"}, + "ENABLE_PROMETHEUS_METRICS": {"type": "boolean"}, + "PROMETHEUS_MULTIPROC_DIR": {"type": "string"}, }, } validate(instance=self, schema=schema) diff --git a/gen3workflow/metrics.py b/gen3workflow/metrics.py new file mode 100644 index 0000000..b6e7c4d --- /dev/null +++ b/gen3workflow/metrics.py @@ -0,0 +1,25 @@ +from typing import Any, Dict + +from cdispyutils.metrics import BaseMetrics +from gen3workflow import logger + +from gen3workflow.config import config + + +class Metrics(BaseMetrics): + def __init__( + self, + prometheus_dir: str = config["PROMETHEUS_MULTIPROC_DIR"], + enabled: bool = True, + ) -> None: + logger.info(f"Setting up Metrics with {prometheus_dir=} and {enabled=}") + super().__init__(prometheus_dir=prometheus_dir, enabled=enabled) + + def add_create_task_api_interaction( + self, + **kwargs: Dict[str, Any], + ) -> None: + """ + Add a metric for create_task API interactions + """ + self.increment_counter(name="gen3_workflow_tasks_created", labels=kwargs) diff --git a/gen3workflow/routes/ga4gh_tes.py b/gen3workflow/routes/ga4gh_tes.py index 2251595..0379285 100644 --- a/gen3workflow/routes/ga4gh_tes.py +++ b/gen3workflow/routes/ga4gh_tes.py @@ -32,11 +32,7 @@ async def get_request_body(request: Request): @router.get("/service-info", status_code=HTTP_200_OK) async def service_info(request: Request, auth=Depends(Auth)) -> dict: - try: - token_claims = await auth.get_token_claims() - except Exception: - token_claims = {} - user_id = token_claims.get("sub") + user_id = await auth.get_user_id() logger.info(f"User '{user_id}' getting TES service info") url = f"{config['TES_SERVER_URL']}/service-info" @@ -164,11 +160,7 @@ def apply_view_to_task(view: str, task: dict) -> dict: @router.get("/tasks", status_code=HTTP_200_OK) async def list_tasks(request: Request, auth=Depends(Auth)) -> dict: - try: - token_claims = await auth.get_token_claims() - except Exception: - token_claims = {} - user_id = token_claims.get("sub") + user_id = await auth.get_user_id() logger.info(f"User '{user_id}' listing TES tasks") supported_params = { @@ -231,11 +223,7 @@ async def list_tasks(request: Request, auth=Depends(Auth)) -> dict: @router.get("/tasks/{task_id}", status_code=HTTP_200_OK) async def get_task(request: Request, task_id: str, auth=Depends(Auth)) -> dict: - try: - token_claims = await auth.get_token_claims() - except Exception: - token_claims = {} - user_id = token_claims.get("sub") + user_id = await auth.get_user_id() logger.info(f"User '{user_id}' getting TES task '{task_id}'") supported_params = {"view"} @@ -268,11 +256,7 @@ async def get_task(request: Request, task_id: str, auth=Depends(Auth)) -> dict: @router.post("/tasks/{task_id}:cancel", status_code=HTTP_200_OK) async def cancel_task(request: Request, task_id: str, auth=Depends(Auth)) -> dict: - try: - token_claims = await auth.get_token_claims() - except Exception: - token_claims = {} - user_id = token_claims.get("sub") + user_id = await auth.get_user_id() logger.info(f"User '{user_id}' canceling TES task '{task_id}'") # check if this user has access to delete this task diff --git a/poetry.lock b/poetry.lock index 5b62714..13169cb 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,23 +1,23 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. [[package]] name = "alembic" -version = "1.14.1" +version = "1.15.2" description = "A database migration tool for SQLAlchemy." optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" files = [ - {file = "alembic-1.14.1-py3-none-any.whl", hash = "sha256:1acdd7a3a478e208b0503cd73614d5e4c6efafa4e73518bb60e4f2846a37b1c5"}, - {file = "alembic-1.14.1.tar.gz", hash = "sha256:496e888245a53adf1498fcab31713a469c65836f8de76e01399aa1c3e90dd213"}, + {file = "alembic-1.15.2-py3-none-any.whl", hash = "sha256:2e76bd916d547f6900ec4bb5a90aeac1485d2c92536923d0b138c02b126edc53"}, + {file = "alembic-1.15.2.tar.gz", hash = "sha256:1c72391bbdeffccfe317eefba686cb9a3c078005478885413b95c3b26c57a8a7"}, ] [package.dependencies] Mako = "*" -SQLAlchemy = ">=1.3.0" -typing-extensions = ">=4" +SQLAlchemy = ">=1.4.0" +typing-extensions = ">=4.12" [package.extras] -tz = ["backports.zoneinfo", "tzdata"] +tz = ["tzdata"] [[package]] name = "annotated-types" @@ -32,13 +32,13 @@ files = [ [[package]] name = "anyio" -version = "4.8.0" +version = "4.9.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false python-versions = ">=3.9" files = [ - {file = "anyio-4.8.0-py3-none-any.whl", hash = "sha256:b5011f270ab5eb0abf13385f851315585cc37ef330dd88e27ec3d34d651fd47a"}, - {file = "anyio-4.8.0.tar.gz", hash = "sha256:1d9fe889df5212298c0c0723fa20479d1b94883a2df44bd3897aa91083316f7a"}, + {file = "anyio-4.9.0-py3-none-any.whl", hash = "sha256:9f76d541cad6e36af7beb62e978876f3b41e3e04f2c1fbf0884604c0a9c4d93c"}, + {file = "anyio-4.9.0.tar.gz", hash = "sha256:673c0c244e15788651a4ff38710fea9675823028a6f08a5eda409e0c9840a028"}, ] [package.dependencies] @@ -48,8 +48,8 @@ sniffio = ">=1.1" typing_extensions = {version = ">=4.5", markers = "python_version < \"3.13\""} [package.extras] -doc = ["Sphinx (>=7.4,<8.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx_rtd_theme"] -test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "trustme", "truststore (>=0.9.1)", "uvloop (>=0.21)"] +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]] @@ -131,32 +131,32 @@ test = ["distro (>=1.9.0,<1.10.0)", "flake8 (>=6.1,<7.0)", "flake8-pyi (>=24.1.0 [[package]] name = "attrs" -version = "25.1.0" +version = "25.3.0" description = "Classes Without Boilerplate" optional = false python-versions = ">=3.8" files = [ - {file = "attrs-25.1.0-py3-none-any.whl", hash = "sha256:c75a69e28a550a7e93789579c22aa26b0f5b83b75dc4e08fe092980051e1090a"}, - {file = "attrs-25.1.0.tar.gz", hash = "sha256:1c97078a80c814273a76b2a298a932eb681c87415c11dee0a6921de7f1b02c3e"}, + {file = "attrs-25.3.0-py3-none-any.whl", hash = "sha256:427318ce031701fea540783410126f03899a97ffc6f61596ad581ac2e40e3bc3"}, + {file = "attrs-25.3.0.tar.gz", hash = "sha256:75d7cefc7fb576747b2c81b4442d4d4a1ce0900973527c011d1030fd3bf4af1b"}, ] [package.extras] benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"] cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit-uv", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"] +docs = ["cogapp", "furo", "myst-parser", "sphinx", 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"typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"}, - {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"}, + {file = "typing_extensions-4.13.2-py3-none-any.whl", hash = "sha256:a439e7c04b49fec3e5d3e2beaa21755cadbbdc391694e28ccdd36ca4a1408f8c"}, + {file = "typing_extensions-4.13.2.tar.gz", hash = "sha256:e6c81219bd689f51865d9e372991c540bda33a0379d5573cddb9a3a23f7caaef"}, ] +[[package]] +name = "typing-inspection" +version = "0.4.0" +description = "Runtime typing introspection tools" +optional = false +python-versions = ">=3.9" +files = [ + {file = "typing_inspection-0.4.0-py3-none-any.whl", hash = "sha256:50e72559fcd2a6367a19f7a7e610e6afcb9fac940c650290eed893d61386832f"}, + {file = "typing_inspection-0.4.0.tar.gz", hash = "sha256:9765c87de36671694a67904bf2c96e395be9c6439bb6c87b5142569dcdd65122"}, +] + +[package.dependencies] +typing-extensions = ">=4.12.0" + [[package]] name = "urllib3" version = "1.26.20" @@ -1800,13 +1909,13 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [[package]] name = "urllib3" -version = "2.3.0" +version = "2.4.0" description = "HTTP library with thread-safe connection pooling, file post, and more." optional = false python-versions = ">=3.9" files = [ - {file = "urllib3-2.3.0-py3-none-any.whl", hash = "sha256:1cee9ad369867bfdbbb48b7dd50374c0967a0bb7710050facf0dd6911440e3df"}, - {file = "urllib3-2.3.0.tar.gz", hash = "sha256:f8c5449b3cf0861679ce7e0503c7b44b5ec981bec0d1d3795a07f1ba96f0204d"}, + {file = "urllib3-2.4.0-py3-none-any.whl", hash = "sha256:4e16665048960a0900c702d4a66415956a584919c03361cac9f1df5c5dd7e813"}, + {file = "urllib3-2.4.0.tar.gz", hash = "sha256:414bc6535b787febd7567804cc015fee39daab8ad86268f1310a9250697de466"}, ] [package.extras] @@ -1817,13 +1926,13 @@ zstd = ["zstandard (>=0.18.0)"] [[package]] name = "uvicorn" -version = "0.34.0" +version = "0.34.1" description = "The lightning-fast ASGI server." optional = false python-versions = ">=3.9" files = [ - {file = "uvicorn-0.34.0-py3-none-any.whl", hash = "sha256:023dc038422502fa28a09c7a30bf2b6991512da7dcdb8fd35fe57cfc154126f4"}, - {file = "uvicorn-0.34.0.tar.gz", hash = "sha256:404051050cd7e905de2c9a7e61790943440b3416f49cb409f965d9dcd0fa73e9"}, + {file = "uvicorn-0.34.1-py3-none-any.whl", hash = "sha256:984c3a8c7ca18ebaad15995ee7401179212c59521e67bfc390c07fa2b8d2e065"}, + {file = "uvicorn-0.34.1.tar.gz", hash = "sha256:af981725fc4b7ffc5cb3b0e9eda6258a90c4b52cb2a83ce567ae0a7ae1757afc"}, ] [package.dependencies] @@ -1862,7 +1971,26 @@ files = [ {file = "xmltodict-0.14.2.tar.gz", hash = "sha256:201e7c28bb210e374999d1dde6382923ab0ed1a8a5faeece48ab525b7810a553"}, ] +[[package]] +name = "zipp" +version = "3.21.0" +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"}, +] + +[package.extras] +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"] +type = ["pytest-mypy"] + [metadata] lock-version = "2.0" python-versions = ">=3.9,<4" -content-hash = "53f47b12e26333bed2da5ea3567cf7f3b3990aba550ec2f4143415dcc5f39351" +content-hash = "59de96f38f98da43f9cc316ca6f1a6205681093075e5f2dca46197ff37fc3def" diff --git a/pyproject.toml b/pyproject.toml index 741bff0..c0c8a5c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,8 +25,9 @@ httpx = "<1" jsonschema = "<5" sqlalchemy = { extras = ["asyncio"], version = "<3" } uvicorn = "<1" +cdispyutils = "^2.4.0" -[tool.poetry.dev-dependencies] +[tool.poetry.group.dev.dependencies] freezegun = "<2" moto = "<6" pytest = "<9" diff --git a/tests/test_metrics.py b/tests/test_metrics.py new file mode 100644 index 0000000..e56e1db --- /dev/null +++ b/tests/test_metrics.py @@ -0,0 +1,23 @@ +import pytest +from unittest.mock import patch +from gen3workflow.app import app +from gen3workflow.config import config + + +@pytest.mark.asyncio +@pytest.mark.parametrize("endpoint", ["/", "/_status", "/ga4gh/tes/v1/tasks"]) +async def test_metrics_collection(client, endpoint): + """ + When metrics are enabled, metrics methods are called for endpoints present in `'/ga4gh/tes/v1/tasks'`. + """ + + # Metrics is currently enabled only for '/ga4gh/tes/v1/tasks' endpoint (hardcoded in the middleware) + with patch( + "gen3workflow.metrics.Metrics.add_create_task_api_interaction" + ) as mock_metrics: + if endpoint == "/ga4gh/tes/v1/tasks": + await client.post(endpoint, json={"name": "test_task"}) + mock_metrics.assert_called_once() + else: + await client.get(endpoint) + mock_metrics.assert_not_called()