feat: OpenAPI schema + interactive docs

bento_reference_service/authz.py

@@ -1,3 +1,4 @@
+import re
 from bento_lib.auth.middleware.fastapi import FastApiAuthMiddleware
 from .config import get_config
 from .logger import get_logger
@@ -8,4 +9,11 @@
 
 # Non-standard middleware setup so that we can import the instance and use it for dependencies too
 config = get_config()  # TODO: Find a way to DI this
-authz_middleware = FastApiAuthMiddleware.build_from_pydantic_config(config, get_logger(config))
+authz_middleware = FastApiAuthMiddleware.build_from_pydantic_config(
+    config,
+    get_logger(config),
+    exempt_request_patterns=(
+        (r"GET", re.escape(config.service_docs_path)),
+        (r"GET", re.escape(config.service_openapi_path)),
+    ),
+)

bento_reference_service/config.py

@@ -19,6 +19,9 @@ class Config(BentoBaseConfig):
     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
 
+    service_docs_path: str = "/docs"
+    service_openapi_path: str = "/openapi.json"
+
     database_uri: str = "postgres://localhost:5432"
     file_ingest_tmp_dir: Path = Path(__file__).parent.parent / "tmp"  # Default to repository `tmp` folder
     file_ingest_chunk_size: int = 1024 * 256  # 256 KiB at a time

bento_reference_service/constants.py

@@ -1,4 +1,6 @@
 import re
+from bento_lib.service_info.constants import SERVICE_GROUP_BENTO
+from bento_lib.service_info.helpers import build_bento_service_type
 from bento_reference_service import __version__
 
 __all__ = [
@@ -11,13 +13,9 @@
 
 BENTO_SERVICE_KIND = "reference"
 
-SERVICE_GROUP = "ca.c3g.bento"
+SERVICE_GROUP = SERVICE_GROUP_BENTO
 SERVICE_ARTIFACT = BENTO_SERVICE_KIND
 
-SERVICE_TYPE = {
-    "group": SERVICE_GROUP,
-    "artifact": SERVICE_ARTIFACT,
-    "version": __version__,
-}
+SERVICE_TYPE = build_bento_service_type(SERVICE_ARTIFACT, __version__)
 
 RANGE_HEADER_PATTERN = re.compile(r"^bytes=(\d+)-(\d+)?$")

bento_reference_service/main.py

@@ -2,6 +2,7 @@
 from fastapi import FastAPI
 from fastapi.middleware.cors import CORSMiddleware
 from fastapi.exceptions import RequestValidationError, StarletteHTTPException
+from urllib.parse import urlparse
 
 from bento_lib.responses.fastapi_errors import (
     http_exception_handler_factory,
@@ -37,7 +38,14 @@ async def lifespan(_app: FastAPI):
     yield
 
 
-app = FastAPI(lifespan=lifespan)
+app = FastAPI(
+    title=config_for_setup.service_name,
+    root_path=urlparse(config_for_setup.service_url_base_path).path,
+    docs_url=config_for_setup.service_docs_path,
+    openapi_url=config_for_setup.service_openapi_path,
+    version=__version__,
+    lifespan=lifespan,
+)
 
 # Attach different routers to the app, for:
 # - genome listing

pyproject.toml

@@ -27,7 +27,7 @@ classifiers = [
 python = "^3.10.0"
 fastapi = "^0.111.0"
 pydantic = "^2.6.1"
-bento-lib = {extras = ["fastapi"], version = "^11.7.2"}
+bento-lib = {extras = ["fastapi"], version = "^11.9.0"}
 aiofiles = "^23.2.1"
 pysam = "~0.22.0"
 jsonschema = "^4.21.1"