Merge pull request #53 from bento-platform/chore/updates

chore: update dependencies, base img, actions

.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 }}
 

.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 }}
 
@@ -34,7 +34,9 @@ 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@v3
+      uses: codecov/codecov-action@v4
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

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
 

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 +38,13 @@ 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:[email protected]",
-        "version": bento_aggregation_service.__version__,
-        "bento": {
+    return await build_service_info_from_pydantic_config(
+        config,
+        logger,
+        {
             "serviceKind": BENTO_SERVICE_KIND,
+            "gitRepository": "https://github.com/bento-platform/bento_aggregation_service",
         },
-        "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
+        SERVICE_TYPE,
+        __version__,
+    )

bento_aggregation_service/config.py

@@ -1,12 +1,9 @@
-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
+from .constants import SERVICE_NAME, SERVICE_TYPE
 
 __all__ = [
     "Config",
@@ -15,46 +12,17 @@
 ]
 
 
-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]))
+    service_name: str = SERVICE_NAME
 
     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:

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

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."
 LABEL devcontainer.metadata='[{ \
@@ -14,7 +14,7 @@ LABEL devcontainer.metadata='[{ \
 # Run as root in the Dockerfile until we drop down to the service user in the entrypoint
 USER root
 
-RUN pip install --no-cache-dir "uvicorn[standard]==0.23.2"
+RUN pip install --no-cache-dir "uvicorn[standard]==0.27.1"
 
 WORKDIR /aggregation