chore: update to bento_lib 10.1 + factor out new shared stuff

bento_reference_service/config.py

@@ -1,5 +1,6 @@
 import json
 
+from bento_lib.logging import LogLevelLiteral
 from fastapi import Depends
 from functools import lru_cache
 from pathlib import Path
@@ -37,6 +38,8 @@ class Config(BaseSettings):
     service_description: str = "Reference data (genomes & annotations) service for the Bento platform."
     service_url_base_path: str = "http://127.0.0.1:5000"  # Base path to construct URIs from
 
+    log_level: LogLevelLiteral = "debug"
+
     database_uri: str = "postgres://localhost:5432"
     data_path: Path = Path(__file__).parent / "data"
 

bento_reference_service/db.py

@@ -1,60 +1,17 @@
-import aiofiles
-import asyncpg
-import contextlib
-
+from bento_lib.db.pg_async import PgAsyncDatabase
 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
 
 
 SCHEMA_PATH = Path(__file__).parent / "sql" / "schema.sql"
 
 
-class Database:
-    def __init__(self, db_uri: str, schema_path: Path):
-        self._db_uri: str = db_uri
-        self._schema_path: Path = schema_path
-
-        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(self._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
+class Database(PgAsyncDatabase):
+    pass  # TODO
 
 
 @lru_cache()

pyproject.toml

@@ -27,7 +27,7 @@ classifiers = [
 python = "^3.10.0"
 fastapi = "^0.104.1"
 pydantic = "^2.5.1"
-bento-lib = {extras = ["fastapi"], version = "^10.0.0"}
+bento-lib = {extras = ["asyncpg", "fastapi"], version = "^10.1.0"}
 aiofiles = "^23.2.1"
 pysam = "^0.22.0"
 elasticsearch = {extras = ["async"], version = "^8.6.0"}