From 622eeec230966706ff76f3f3256c35e1777ca88f Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 12 Feb 2024 11:44:34 -0500 Subject: [PATCH 1/5] chore: update dependencies, base img, actions --- .github/workflows/lint.yml | 4 +- .github/workflows/test.yml | 8 +- .idea/misc.xml | 3 + Dockerfile | 4 +- bento_aggregation_service/app.py | 49 +- bento_aggregation_service/config.py | 39 +- bento_aggregation_service/service_manager.py | 2 +- dev.Dockerfile | 4 +- poetry.lock | 1759 +++++++++--------- pyproject.toml | 14 +- 10 files changed, 931 insertions(+), 955 deletions(-) diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index e19c909..43e1be5 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.10", "3.11"] + python-version: ["3.10", "3.12"] steps: @@ -23,7 +23,7 @@ jobs: submodules: true - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 2578d4c..b8fba4a 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.10", "3.11"] + python-version: ["3.10", "3.12"] steps: @@ -23,7 +23,7 @@ jobs: submodules: true - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} @@ -37,4 +37,6 @@ jobs: run: poetry run coverage run -m unittest -v - name: Upload coverage to Codecov - uses: codecov/codecov-action@v3 + uses: codecov/codecov-action@v4 + env: + CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} diff --git a/.idea/misc.xml b/.idea/misc.xml index ec3f0dc..597d5c0 100644 --- a/.idea/misc.xml +++ b/.idea/misc.xml @@ -1,5 +1,8 @@ + + diff --git a/Dockerfile b/Dockerfile index ae4485f..854bb1e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,11 +1,11 @@ -FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.10.20 +FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.02.01 # Run as root in the Dockerfile until we drop down to the service user in the entrypoint USER root # Use uvicorn (instead of hypercorn) in production since I've found # multiple benchmarks showing it to be faster - David L -RUN pip install --no-cache-dir "uvicorn[standard]==0.23.2" +RUN pip install --no-cache-dir "uvicorn[standard]==0.27.1" WORKDIR /aggregation diff --git a/bento_aggregation_service/app.py b/bento_aggregation_service/app.py index cc3c859..c61cd70 100644 --- a/bento_aggregation_service/app.py +++ b/bento_aggregation_service/app.py @@ -1,18 +1,14 @@ from __future__ import annotations import asyncio -import bento_aggregation_service -from bento_lib.types import GA4GHServiceInfo +from bento_lib.service_info.helpers import build_service_info_from_pydantic_config from fastapi import FastAPI from fastapi.middleware.cors import CORSMiddleware +from . import __version__ from .config import ConfigDependency, get_config -from .constants import ( - BENTO_SERVICE_KIND, - SERVICE_TYPE, - SERVICE_NAME, -) +from .constants import BENTO_SERVICE_KIND, SERVICE_TYPE from .logger import LoggerDependency from .search.handlers.datasets import dataset_search_router @@ -42,40 +38,5 @@ async def _git_stdout(*args) -> str: @application.get("/service-info") async def service_info(config: ConfigDependency, logger: LoggerDependency): - info: GA4GHServiceInfo = { - "id": config.service_id, - "name": SERVICE_NAME, # TODO: Should be globally unique? - "type": SERVICE_TYPE, - "description": "Aggregation service for a Bento platform node.", - "organization": { - "name": "C3G", - "url": "https://www.computationalgenomics.ca" - }, - "contactUrl": "mailto:info@c3g.ca", - "version": bento_aggregation_service.__version__, - "bento": { - "serviceKind": BENTO_SERVICE_KIND, - }, - "environment": "prod", - } - - if not config.bento_debug: - return info - - info["environment"] = "dev" - - try: - if res_tag := await _git_stdout("describe", "--tags", "--abbrev=0"): - # noinspection PyTypeChecker - info["bento"]["gitTag"] = res_tag - if res_branch := await _git_stdout("branch", "--show-current"): - # noinspection PyTypeChecker - info["bento"]["gitBranch"] = res_branch - if res_commit := await _git_stdout("rev-parse", "HEAD"): - # noinspection PyTypeChecker - info["bento"]["gitCommit"] = res_commit - - except Exception as e: - logger.warning(f"Could not retrieve git information: {type(e).__name__}") - - return info + return build_service_info_from_pydantic_config( + config, logger, {"serviceKind": BENTO_SERVICE_KIND}, SERVICE_TYPE, __version__) diff --git a/bento_aggregation_service/config.py b/bento_aggregation_service/config.py index e31b038..211d81a 100644 --- a/bento_aggregation_service/config.py +++ b/bento_aggregation_service/config.py @@ -1,10 +1,7 @@ -import json - +from bento_lib.config.pydantic import BentoBaseConfig from fastapi import Depends from functools import lru_cache -from pydantic.fields import FieldInfo -from pydantic_settings import BaseSettings, EnvSettingsSource, PydanticBaseSettingsSource, SettingsConfigDict -from typing import Annotated, Any, Literal +from typing import Annotated from .constants import SERVICE_TYPE @@ -15,46 +12,16 @@ ] -class CorsOriginsParsingSource(EnvSettingsSource): - def prepare_field_value(self, field_name: str, field: FieldInfo, value: Any, value_is_complex: bool) -> Any: - if field_name == "cors_origins": - return tuple(x.strip() for x in value.split(";")) if value is not None else () - return json.loads(value) if value_is_complex else value - - -class Config(BaseSettings): - bento_debug: bool = False - +class Config(BentoBaseConfig): service_id: str = str(":".join(list(SERVICE_TYPE.values())[:2])) request_timeout: int = 180 # seconds - bento_authz_service_url: str # Bento authorization service base URL - authz_enabled: bool = True - # Other services - settings and flags use_gohan: bool = False katsu_url: str service_registry_url: str # used for fetching list of data services, so we can get data type providers - cors_origins: tuple[str, ...] = ("*",) - - log_level: Literal["debug", "info", "warning", "error"] = "debug" - - # Make Config instances hashable + immutable - model_config = SettingsConfigDict(frozen=True) - - @classmethod - def settings_customise_sources( - cls, - settings_cls: type[BaseSettings], - init_settings: PydanticBaseSettingsSource, - env_settings: PydanticBaseSettingsSource, - dotenv_settings: PydanticBaseSettingsSource, - file_secret_settings: PydanticBaseSettingsSource, - ) -> tuple[PydanticBaseSettingsSource, ...]: - return (CorsOriginsParsingSource(settings_cls),) - @lru_cache() def get_config() -> Config: diff --git a/bento_aggregation_service/service_manager.py b/bento_aggregation_service/service_manager.py index 079da7a..4631c91 100644 --- a/bento_aggregation_service/service_manager.py +++ b/bento_aggregation_service/service_manager.py @@ -3,7 +3,7 @@ import contextlib import logging -from bento_lib.types import GA4GHServiceInfo +from bento_lib.service_info.types import GA4GHServiceInfo from fastapi import Depends from functools import lru_cache from typing import Annotated, AsyncIterator diff --git a/dev.Dockerfile b/dev.Dockerfile index 423aad3..7eaacdf 100644 --- a/dev.Dockerfile +++ b/dev.Dockerfile @@ -1,4 +1,4 @@ -FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.10.20 +FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.02.01 LABEL org.opencontainers.image.description="Local development image the Bento aggregation service." 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["fastapi"], version = "^8.1.0"} -fastapi = "^0.103.0" -pydantic-settings = "^2.0.3" +bento-lib = {extras = ["fastapi"], version = "^11.4.0"} +fastapi = "^0.109.2" +pydantic-settings = "^2.1.0" aiohttp = "^3.9.2" -pydantic = "^2.4.2" +pydantic = "^2.6.1" [tool.poetry.group.dev.dependencies] coverage = "^7.3.2" debugpy = "^1.8.0" -flake8 = "^6.0.0" -pytest = "^7.4.3" +flake8 = "^7.0.0" +pytest = "^7.4.4" pytest-cov = "^4.1.0" tox = "^4.11.3" -httpx = "^0.24.1" +httpx = "^0.26.0" From 027c1e509f2f5353c0b06db1ee72a005d7e9a644 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 12 Feb 2024 11:48:41 -0500 Subject: [PATCH 2/5] chore: bump version to 0.19.3 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 600909f..4483933 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api" [tool.poetry] name = "bento_aggregation_service" -version = "0.19.2" +version = "0.19.3" description = "Search result aggregation service for the Bento platform." authors = ["David Lougheed "] readme = "README.md" From c4916c3d5d611535b01ed6398e2546cd91ce1557 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 12 Feb 2024 11:55:09 -0500 Subject: [PATCH 3/5] ci: fix running tests --- .github/workflows/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index b8fba4a..35422b6 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -34,7 +34,7 @@ jobs: run: python -m poetry install - name: Test - run: poetry run coverage run -m unittest -v + run: poetry run pytest -svv --cov=bento_aggregation_service --cov-branch - name: Upload coverage to Codecov uses: codecov/codecov-action@v4 From 618983d6ada28023094dc96768a1aa4bee51b4ac Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 12 Feb 2024 11:55:23 -0500 Subject: [PATCH 4/5] fix: issues caught by testing /service-info --- bento_aggregation_service/app.py | 2 +- bento_aggregation_service/config.py | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/bento_aggregation_service/app.py b/bento_aggregation_service/app.py index c61cd70..0e03d76 100644 --- a/bento_aggregation_service/app.py +++ b/bento_aggregation_service/app.py @@ -38,5 +38,5 @@ async def _git_stdout(*args) -> str: @application.get("/service-info") async def service_info(config: ConfigDependency, logger: LoggerDependency): - return build_service_info_from_pydantic_config( + return await build_service_info_from_pydantic_config( config, logger, {"serviceKind": BENTO_SERVICE_KIND}, SERVICE_TYPE, __version__) diff --git a/bento_aggregation_service/config.py b/bento_aggregation_service/config.py index 211d81a..ac6becf 100644 --- a/bento_aggregation_service/config.py +++ b/bento_aggregation_service/config.py @@ -3,7 +3,7 @@ from functools import lru_cache from typing import Annotated -from .constants import SERVICE_TYPE +from .constants import SERVICE_NAME, SERVICE_TYPE __all__ = [ "Config", @@ -14,6 +14,7 @@ class Config(BentoBaseConfig): service_id: str = str(":".join(list(SERVICE_TYPE.values())[:2])) + service_name: str = SERVICE_NAME request_timeout: int = 180 # seconds From ae534e118a9f80b62e139b423f1f83de9363323f Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 12 Feb 2024 13:20:02 -0500 Subject: [PATCH 5/5] chore: add git repository to service info response --- bento_aggregation_service/app.py | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/bento_aggregation_service/app.py b/bento_aggregation_service/app.py index 0e03d76..7e09654 100644 --- a/bento_aggregation_service/app.py +++ b/bento_aggregation_service/app.py @@ -39,4 +39,12 @@ async def _git_stdout(*args) -> str: @application.get("/service-info") async def service_info(config: ConfigDependency, logger: LoggerDependency): return await build_service_info_from_pydantic_config( - config, logger, {"serviceKind": BENTO_SERVICE_KIND}, SERVICE_TYPE, __version__) + config, + logger, + { + "serviceKind": BENTO_SERVICE_KIND, + "gitRepository": "https://github.com/bento-platform/bento_aggregation_service", + }, + SERVICE_TYPE, + __version__, + )