Merge pull request #39 from bento-platform/chore/update

chore: update bento_lib (w/ refactors) + dependencies + images

Dockerfile

@@ -1,8 +1,8 @@
-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
-RUN pip install --no-cache-dir poetry==1.6.1 "uvicorn[standard]==0.24.0"
+RUN pip install --no-cache-dir poetry==1.7.1 "uvicorn[standard]==0.25.0"
 
 # Backwards-compatible with old BentoV2 container layout
 WORKDIR /drop-box

bento_drop_box_service/config.py

@@ -1,11 +1,7 @@
-import json
-
-from bento_lib.logging import LogLevelLiteral
+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, Literal
 
 from .constants import SERVICE_TYPE
 
@@ -16,48 +12,18 @@
 ]
 
 
-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
-    bento_container_local: bool = False
-
+class Config(BentoBaseConfig):
     service_id: str = str(":".join(list(SERVICE_TYPE.values())[:2]))
     service_name: str = "Bento Drop Box Service"
     service_description: str = "Drop box service for a Bento platform node."
-    service_contact_url: str = "mailto:[email protected]"
     service_url: str = "http://127.0.0.1:5000"  # base URL to construct object URIs from
 
     service_data: str = "data/"
     service_data_source: Literal["local"] = "local"
     traversal_limit: int = 16
 
-    bento_authz_service_url: str  # Bento authorization service base URL
     authz_enabled: bool = True
 
-    cors_origins: tuple[str, ...]
-
-    log_level: LogLevelLiteral = "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_drop_box_service/constants.py

@@ -1,4 +1,4 @@
-from bento_lib.service_info import GA4GHServiceType
+from bento_lib.service_info.types import GA4GHServiceType
 from bento_drop_box_service import __version__
 
 __all__ = [

bento_drop_box_service/routes.py

@@ -1,6 +1,6 @@
 from bento_lib.auth.permissions import P_VIEW_DROP_BOX, P_INGEST_DROP_BOX, P_DELETE_DROP_BOX
 from bento_lib.auth.resources import RESOURCE_EVERYTHING
-from bento_lib.service_info import SERVICE_ORGANIZATION_C3G, build_service_info
+from bento_lib.service_info.helpers import build_service_info_from_pydantic_config
 from fastapi import APIRouter, Form, Request, status
 from fastapi.exceptions import HTTPException
 from fastapi.responses import JSONResponse
@@ -74,15 +74,13 @@ async def drop_box_delete(path: str, backend: BackendDependency):
 @drop_box_router.get("/service-info", dependencies=[authz_middleware.dep_public_endpoint()])
 async def service_info(config: ConfigDependency, logger: LoggerDependency) -> Response:
     # Spec: https://github.com/ga4gh-discovery/ga4gh-service-info
-    return JSONResponse(await build_service_info({
-        "id": config.service_id,
-        "name": config.service_name,
-        "type": SERVICE_TYPE,
-        "description": config.service_description,
-        "organization": SERVICE_ORGANIZATION_C3G,
-        "contactUrl": config.service_contact_url,
-        "version": __version__,
-        "bento": {
-            "serviceKind": BENTO_SERVICE_KIND
+    return JSONResponse(await build_service_info_from_pydantic_config(
+        config,
+        logger,
+        {
+            "serviceKind": BENTO_SERVICE_KIND,
+            "gitRepository": "https://github.com/bento-platform/bento_drop_box_service",
         },
-    }, debug=config.bento_debug, local=config.bento_container_local, logger=logger))
+        SERVICE_TYPE,
+        __version__,
+    ))

dev.Dockerfile

@@ -1,6 +1,6 @@
-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 poetry==1.6.1 "uvicorn[standard]==0.24.0"
+RUN pip install --no-cache-dir poetry==1.7.1 "uvicorn[standard]==0.25.0"
 
 # Backwards-compatible with old BentoV2 container layout
 WORKDIR /drop-box