chore: update bento_lib + use new lib utils + update base imgs

Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.11.10
+FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.12.01
 
 # Use uvicorn (instead of hypercorn) in production since I've found
 # multiple benchmarks showing it to be faster - David L

bento_authorization_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_GROUP, SERVICE_ARTIFACT
 
@@ -15,23 +12,15 @@
 ]
 
 
-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):
+    # the superclass has this as a required field - we ignore it since this IS the authz service
+    # TODO: should this maybe be a [str | None] in bento_lib?
+    bento_authz_service_url: str = ""
 
     service_id: str = f"{SERVICE_GROUP}:{SERVICE_ARTIFACT}"
     service_name: str = "Bento Authorization Service"
     service_url_base_path: str = "http://127.0.0.1:5000"  # Base path to construct URIs from
 
-    # /service-info customization
-    service_contact_url: str = "mailto:[email protected]"
-
     database_uri: str = "postgres://localhost:5432"
 
     # OpenID well-known URL of the instance Identity Provider to extract endpoints from
@@ -44,24 +33,6 @@ class Config(BaseSettings):
     #  - Default set of disabled 'insecure' algorithms (in this case symmetric key algorithms)
     disabled_token_signing_algorithms: frozenset = frozenset(["HS256", "HS384", "HS512"])
 
-    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_authorization_service/db.py

@@ -1,13 +1,12 @@
-import aiofiles
 import asyncpg
-import contextlib
 import json
 
+from bento_lib.db.pg_async import PgAsyncDatabase
 from datetime import datetime
 from fastapi import Depends
 from functools import lru_cache
 from pathlib import Path
-from typing import Annotated, AsyncGenerator
+from typing import Annotated
 
 from .config import ConfigDependency
 from .models import SubjectModel, ResourceModel, GrantModel, StoredGrantModel, GroupModel, StoredGroupModel
@@ -73,46 +72,9 @@ def group_db_deserialize(r: asyncpg.Record | None) -> StoredGroupModel | None:
     )
 
 
-class Database:
+class Database(PgAsyncDatabase):
     def __init__(self, db_uri: str):
-        self._db_uri: str = db_uri
-        self._pool: asyncpg.Pool | None = None
-
-    async def initialize(self, pool_size: int = 10):
-        conn: asyncpg.Connection
-
-        if not self._pool:  # Initialize the connection pool if needed
-            self._pool = await asyncpg.create_pool(self._db_uri, min_size=pool_size, max_size=pool_size)
-
-        # Connect to the database and execute the schema script
-        async with aiofiles.open(SCHEMA_PATH, "r") as sf:
-            async with self.connect() as conn:
-                async with conn.transaction():
-                    await conn.execute(await sf.read())
-
-    async def close(self):
-        if self._pool:
-            await self._pool.close()
-            self._pool = None
-
-    @contextlib.asynccontextmanager
-    async def connect(
-        self,
-        existing_conn: asyncpg.Connection | None = None,
-    ) -> AsyncGenerator[asyncpg.Connection, None]:
-        # TODO: raise raise DatabaseError("Pool is not available") when FastAPI has lifespan dependencies
-        #  + manage pool lifespan in lifespan fn.
-
-        if self._pool is None:
-            await self.initialize()  # initialize if this is the first time we're using the pool
-
-        if existing_conn is not None:
-            yield existing_conn
-            return
-
-        conn: asyncpg.Connection
-        async with self._pool.acquire() as conn:
-            yield conn
+        super().__init__(db_uri, SCHEMA_PATH)
 
     async def get_subject(self, id_: int) -> SubjectModel | None:
         conn: asyncpg.Connection

bento_authorization_service/main.py

@@ -1,7 +1,6 @@
-import asyncio
-
 from bento_lib.responses.fastapi_errors import http_exception_handler_factory, validation_exception_handler_factory
-from bento_lib.types import BentoExtraServiceInfo
+from bento_lib.service_info.helpers import build_service_info_from_pydantic_config
+from bento_lib.service_info.types import BentoExtraServiceInfo
 from fastapi import FastAPI, Request, Response, status
 from fastapi.exceptions import RequestValidationError
 from fastapi.middleware.cors import CORSMiddleware
@@ -67,47 +66,11 @@ async def permissions_enforcement(request: Request, call_next) -> Response:
     return response
 
 
-async def _git_stdout(*args) -> str:
-    git_proc = await asyncio.create_subprocess_exec(
-        "git", *args, stdout=asyncio.subprocess.PIPE, stderr=asyncio.subprocess.PIPE
-    )
-    res, _ = await git_proc.communicate()
-    return res.decode().rstrip()
-
-
 @app.get("/service-info", dependencies=[public_endpoint_dependency])
 async def service_info(config: ConfigDependency):
     bento_info: BentoExtraServiceInfo = {
         "serviceKind": BENTO_SERVICE_KIND,
         "dataService": False,
         "gitRepository": "https://github.com/bento-platform/bento_authorization_service",
     }
-
-    debug_mode = config.bento_debug
-    if debug_mode:  # pragma: no cover
-        try:
-            if res_tag := await _git_stdout("describe", "--tags", "--abbrev=0"):
-                # noinspection PyTypeChecker
-                bento_info["gitTag"] = res_tag
-            if res_branch := await _git_stdout("branch", "--show-current"):
-                # noinspection PyTypeChecker
-                bento_info["gitBranch"] = res_branch
-            if res_commit := await _git_stdout("rev-parse", "HEAD"):
-                # noinspection PyTypeChecker
-                bento_info["gitCommit"] = res_commit
-
-        except Exception as e:
-            logger.error(f"Error retrieving git information: {type(e).__name__}")
-
-    # Public endpoint, no permissions checks required
-    return {
-        "id": config.service_id,
-        "name": config.service_name,  # TODO: Should be globally unique?
-        "type": SERVICE_TYPE,
-        "description": "Authorization & permissions service for the Bento platform.",
-        "organization": {"name": "C3G", "url": "https://www.computationalgenomics.ca"},
-        "contactUrl": config.service_contact_url,
-        "version": __version__,
-        "environment": "dev" if debug_mode else "prod",
-        "bento": bento_info,
-    }
+    return await build_service_info_from_pydantic_config(config, logger, bento_info, SERVICE_TYPE, __version__)

bento_authorization_service/utils.py

@@ -4,5 +4,5 @@
 __all__ = ["json_model_dump_kwargs"]
 
 
-def json_model_dump_kwargs(x: BaseModel, **kwargs):
+def json_model_dump_kwargs(x: BaseModel, **kwargs) -> str:
     return json.dumps(x.model_dump(mode="json"), **kwargs)

dev.Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.11.10
+FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.12.01
 
 RUN pip install --no-cache-dir -U pip && pip install --no-cache-dir "uvicorn[standard]==0.24.0"